data_EMD-0089
# 
_entry.id   EMD-0089 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.398 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   6GYB         pdb_00006gyb 10.2210/pdb6gyb/pdb 
WWPDB D_1200010684 ?            ?                   
EMDB  EMD-0089     ?            ?                   
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.details 
_pdbx_database_related.db_id 
_pdbx_database_related.content_type 
BMRB 'NMR assignments for VirB10 N-teminal domain'                                   27342    unspecified            
EMDB 'Structure of the core complex of a bacterial killing Type IV Secretion System' EMD-0089 'associated EM volume' 
# 
_citation.abstract                  ? 
_citation.abstract_id_CAS           ? 
_citation.book_id_ISBN              ? 
_citation.book_publisher            ? 
_citation.book_publisher_city       ? 
_citation.book_title                ? 
_citation.coordinate_linkage        ? 
_citation.country                   UK 
_citation.database_id_Medline       ? 
_citation.details                   ? 
_citation.id                        primary 
_citation.journal_abbrev            'Nat Microbiol' 
_citation.journal_id_ASTM           ? 
_citation.journal_id_CSD            ? 
_citation.journal_id_ISSN           2058-5276 
_citation.journal_full              ? 
_citation.journal_issue             ? 
_citation.journal_volume            3 
_citation.language                  ? 
_citation.page_first                1429 
_citation.page_last                 1440 
_citation.title                     
'Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri.' 
_citation.year                      2018 
_citation.database_id_CSD           ? 
_citation.pdbx_database_id_DOI      10.1038/s41564-018-0262-z 
_citation.pdbx_database_id_PubMed   30349081 
_citation.unpublished_flag          ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Sgro, G.G.'               1  ? 
primary 'Costa, T.R.D.'            2  ? 
primary 'Cenens, W.'               3  ? 
primary 'Souza, D.P.'              4  ? 
primary 'Cassago, A.'              5  ? 
primary 'Coutinho de Oliveira, L.' 6  ? 
primary 'Salinas, R.K.'            7  ? 
primary 'Portugal, R.V.'           8  ? 
primary 'Farah, C.S.'              9  ? 
primary 'Waksman, G.'              10 ? 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer man VirB7            14762.795 14 ? ? ? ? 
2 polymer man 'VirB9 protein'  29359.385 14 ? ? ? ? 
3 polymer man 'VirB10 protein' 43392.469 14 ? ? ? ? 
# 
loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.pdbx_seq_one_letter_code 
1 'polypeptide(L)' 
;MNPMYVSKLSLVLVAAALVGACATKPAPDFGGRWKHVNHFDEAPTEIPLYTSYTYQATPMDGTLKTMLERWAADSNMQLS
YNLPSDYTLIGPVSAISTTSVQQAATELSAVYAAQGVSVSVSANKLLVQPVPVSSGAKL
;
2 'polypeptide(L)' 
;MKLFNRYRVALLSALPLALCALSAAAQVVQEYEYAPDRIYQVRTGLGITTQVELSPNEKILDYSTGFTGGWELTRRENVF
YLKPKNVDVDTNMMIRTATHSYILELKVVATDWQRLEQAKQAGVQYKVVFTYPKDTSFNNVADADTSKNGPLLNAKILKD
RRYYYDYDYATRTKKSWLIPSRVYDDGKFTYINMDLTRFPTGNFPAVFAREKEHAEDFLVNTTVEGNTLIVHGTYPFLVV
RHGDNVVGLRRNKQK
;
3 'polypeptide(L)' 
;MNSNIPNSPDERIQNHGGDEQHNGDHNERNNPYFARQQASAEPDLDANEPILRSSDIKRLNRKALVFLAAIAALLILAIF
WLATQSGEDSAPPKPRTETVVAPALPQSMTAPVEEAPVPLAQQPSLPPLPPMPTDNSEEVSSAPERQRGPTLLERRILAE
SAANGGGVPGQLGAQPAPTQEDGPVTLAKPISNPDGLLVRGTYIRCILETRIISDFGGYTSCIVTEPVYSINGHNLLLPK
GSKMLGQYSAGEPTSHRLQVVWDRVTTPTGLDVTLMGPGIDTLGSSGHPGNYNAHWGNKIASALFISLLSDAFKYAAAEY
GPETTTIGVGSGIVTQQPFESNTARSMQQLAEQAVEKSGRRPATLTINQGTVLNVYVAKDVDFSAVLPKAAALEGLSAWS
HPQFEK
;
# 
loop_
_entity_src_gen.entity_id 
_entity_src_gen.pdbx_src_id 
_entity_src_gen.pdbx_alt_source_flag 
_entity_src_gen.pdbx_seq_type 
_entity_src_gen.pdbx_beg_seq_num 
_entity_src_gen.pdbx_end_seq_num 
_entity_src_gen.gene_src_common_name 
_entity_src_gen.gene_src_genus 
_entity_src_gen.pdbx_gene_src_gene 
_entity_src_gen.gene_src_species 
_entity_src_gen.gene_src_strain 
_entity_src_gen.gene_src_tissue 
_entity_src_gen.gene_src_tissue_fraction 
_entity_src_gen.gene_src_details 
_entity_src_gen.pdbx_gene_src_fragment 
_entity_src_gen.pdbx_gene_src_scientific_name 
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 
_entity_src_gen.pdbx_gene_src_variant 
_entity_src_gen.pdbx_gene_src_cell_line 
_entity_src_gen.pdbx_gene_src_atcc 
_entity_src_gen.pdbx_gene_src_culture_collection 
_entity_src_gen.pdbx_gene_src_organ 
_entity_src_gen.pdbx_gene_src_organelle 
_entity_src_gen.pdbx_gene_src_cell 
_entity_src_gen.pdbx_gene_src_cellular_location 
_entity_src_gen.host_org_common_name 
_entity_src_gen.pdbx_host_org_scientific_name 
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 
_entity_src_gen.host_org_genus 
_entity_src_gen.pdbx_host_org_gene 
_entity_src_gen.pdbx_host_org_organ 
_entity_src_gen.host_org_species 
_entity_src_gen.pdbx_host_org_tissue 
_entity_src_gen.pdbx_host_org_tissue_fraction 
_entity_src_gen.pdbx_host_org_strain 
_entity_src_gen.pdbx_host_org_variant 
_entity_src_gen.pdbx_host_org_cell_line 
_entity_src_gen.pdbx_host_org_atcc 
_entity_src_gen.pdbx_host_org_culture_collection 
_entity_src_gen.pdbx_host_org_cell 
_entity_src_gen.pdbx_host_org_organelle 
_entity_src_gen.pdbx_host_org_cellular_location 
_entity_src_gen.pdbx_host_org_vector_type 
_entity_src_gen.pdbx_host_org_vector 
_entity_src_gen.host_org_details 
_entity_src_gen.expression_system_id 
_entity_src_gen.plasmid_name 
_entity_src_gen.plasmid_details 
_entity_src_gen.pdbx_description 
1 1 sample 'Biological sequence' 1 139 ? ? XAC2622           ? ?   ? ? ? ? 'Xanthomonas axonopodis pv. citri (strain 306)' 190486 
? ? ? ? ? ? ? ? ? 'Escherichia coli BL21(DE3)' 469008 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
2 1 sample 'Biological sequence' 1 255 ? ? 'virB9, XAC2620'  ? 306 ? ? ? ? 'Xanthomonas axonopodis pv. citri (strain 306)' 190486 
? ? ? ? ? ? ? ? ? 'Escherichia coli BL21(DE3)' 469008 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
3 1 sample 'Biological sequence' 1 406 ? ? 'virB10, XAC2619' ? 306 ? ? ? ? 'Xanthomonas axonopodis pv. citri (strain 306)' 190486 
? ? ? ? ? ? ? ? ? 'Escherichia coli BL21(DE3)' 469008 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
ALA 'L-peptide linking' y ALANINE         ? 'C3 H7 N O2'     89.093  
ARG 'L-peptide linking' y ARGININE        ? 'C6 H15 N4 O2 1' 175.209 
ASN 'L-peptide linking' y ASPARAGINE      ? 'C4 H8 N2 O3'    132.118 
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4'     133.103 
CYS 'L-peptide linking' y CYSTEINE        ? 'C3 H7 N O2 S'   121.158 
GLN 'L-peptide linking' y GLUTAMINE       ? 'C5 H10 N2 O3'   146.144 
GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4'     147.129 
GLY 'peptide linking'   y GLYCINE         ? 'C2 H5 N O2'     75.067  
HIS 'L-peptide linking' y HISTIDINE       ? 'C6 H10 N3 O2 1' 156.162 
ILE 'L-peptide linking' y ISOLEUCINE      ? 'C6 H13 N O2'    131.173 
LEU 'L-peptide linking' y LEUCINE         ? 'C6 H13 N O2'    131.173 
LYS 'L-peptide linking' y LYSINE          ? 'C6 H15 N2 O2 1' 147.195 
MET 'L-peptide linking' y METHIONINE      ? 'C5 H11 N O2 S'  149.211 
PHE 'L-peptide linking' y PHENYLALANINE   ? 'C9 H11 N O2'    165.189 
PRO 'L-peptide linking' y PROLINE         ? 'C5 H9 N O2'     115.130 
SER 'L-peptide linking' y SERINE          ? 'C3 H7 N O3'     105.093 
THR 'L-peptide linking' y THREONINE       ? 'C4 H9 N O3'     119.119 
TRP 'L-peptide linking' y TRYPTOPHAN      ? 'C11 H12 N2 O2'  204.225 
TYR 'L-peptide linking' y TYROSINE        ? 'C9 H11 N O3'    181.189 
VAL 'L-peptide linking' y VALINE          ? 'C5 H11 N O2'    117.146 
# 
_exptl.entry_id         EMD-0089 
_exptl.details          ? 
_exptl.method           'ELECTRON MICROSCOPY' 
_exptl.method_details   ? 
# 
_struct_keywords.entry_id        EMD-0089 
_struct_keywords.text            
'core complex, bacterial killing, protein transport, bacterial Type IV Secretion System, MEMBRANE PROTEIN' 
_struct_keywords.pdbx_keywords   'MEMBRANE PROTEIN' 
_struct_keywords.pdbx_details    ? 
# 
loop_
_struct_ref.id 
_struct_ref.db_name 
_struct_ref.db_code 
_struct_ref.entity_id 
1 UNP Q8PJB3_XANAC 1 
2 UNP Q8PJB5_XANAC 2 
3 UNP Q8PJB6_XANAC 3 
# 
_em_3d_fitting.entry_id          EMD-0089 
_em_3d_fitting.id                1 
_em_3d_fitting.details           
;The electron density was clearly interpretable, which allowed us to build a de novo structural model. This process began by fitting the crystallographic model of the X. citri VirB7 C-terminal N0 domain (PDB:3OV5) and the NMR model of the X. citri VirB9CTD-VirB7NTD complex (PDB:2N01) in order to identify the map with the correct handedness. Models were positioned using Fit in map tool in Chimera, and saved relative to the map. Using these as starting points, we were able to manually build the rest of the model for VirB7 and VirB9CTD, and the de novo models for VirB10CTD, VirB10NTD_150-161 and VirB9NTD using Coot. In this manner, we obtained a combined model for a single VirB7-VirB9-VirB10 heterotrimer unit, which was submitted to iterative rounds of real space refinement and building using PHENIX and Coot software, respectively. Thirteen more copies of the refined heterotrimer were then fit into the density map using Chimera and new rounds of real space refinement (now using NCS for the 42 chains contained in the structure) and building using PHENIX and Coot, respectively, were executed until we obtained good parameters for Ramachandran plot and MolProbity. Chimera and PyMol were used for map and model visualization and figure production.
;
_em_3d_fitting.overall_b_value   138 
_em_3d_fitting.ref_protocol      ? 
_em_3d_fitting.ref_space         REAL 
_em_3d_fitting.target_criteria   'Cross-correlation coefficient' 
_em_3d_fitting.method            ? 
# 
_em_3d_reconstruction.entry_id                    EMD-0089 
_em_3d_reconstruction.id                          1 
_em_3d_reconstruction.algorithm                   'BACK PROJECTION' 
_em_3d_reconstruction.details                     ? 
_em_3d_reconstruction.fsc_type                    'EVEN/ODD MAPS REFINED TOTALLY INDEPENDENT (GOLD STANDARD)' 
_em_3d_reconstruction.refinement_type             ? 
_em_3d_reconstruction.image_processing_id         1 
_em_3d_reconstruction.num_class_averages          1 
_em_3d_reconstruction.num_particles               142306 
_em_3d_reconstruction.resolution                  3.28 
_em_3d_reconstruction.resolution_method           'FSC 0.143 CUT-OFF' 
_em_3d_reconstruction.symmetry_type               POINT 
_em_3d_reconstruction.method                      ? 
_em_3d_reconstruction.nominal_pixel_size          ? 
_em_3d_reconstruction.actual_pixel_size           ? 
_em_3d_reconstruction.magnification_calibration   ? 
_em_3d_reconstruction.citation_id                 ? 
_em_3d_reconstruction.euler_angles_details        ? 
# 
_em_buffer.id            1 
_em_buffer.details       ? 
_em_buffer.pH            8.0 
_em_buffer.specimen_id   1 
_em_buffer.name          ? 
# 
_em_entity_assembly.id                   1 
_em_entity_assembly.parent_id            0 
_em_entity_assembly.details              'Fourteen copies of each of the following three subunits: VirB7, VirB9 and VirB10' 
_em_entity_assembly.go_id                ? 
_em_entity_assembly.name                 'Core complex of a bacterial killing type IV secretion system from Xanthomonas' 
_em_entity_assembly.source               RECOMBINANT 
_em_entity_assembly.type                 COMPLEX 
_em_entity_assembly.entity_id_list       '1, 2, 3' 
_em_entity_assembly.ipr_id               ? 
_em_entity_assembly.synonym              ? 
_em_entity_assembly.number_of_copies     ? 
_em_entity_assembly.oligomeric_details   ? 
_em_entity_assembly.mutant_flag          ? 
# 
_em_image_scans.entry_id                EMD-0089 
_em_image_scans.id                      1 
_em_image_scans.dimension_height        ? 
_em_image_scans.dimension_width         ? 
_em_image_scans.frames_per_image        40 
_em_image_scans.image_recording_id      1 
_em_image_scans.sampling_size           ? 
_em_image_scans.scanner_model           ? 
_em_image_scans.used_frames_per_image   ? 
_em_image_scans.citation_id             ? 
_em_image_scans.number_digital_images   ? 
_em_image_scans.od_range                ? 
_em_image_scans.quant_bit_size          ? 
_em_image_scans.details                 ? 
# 
_em_imaging.id                              1 
_em_imaging.entry_id                        EMD-0089 
_em_imaging.accelerating_voltage            300 
_em_imaging.alignment_procedure             ? 
_em_imaging.c2_aperture_diameter            ? 
_em_imaging.calibrated_defocus_max          ? 
_em_imaging.calibrated_defocus_min          ? 
_em_imaging.calibrated_magnification        ? 
_em_imaging.cryogen                         ? 
_em_imaging.details                         ? 
_em_imaging.electron_source                 'FIELD EMISSION GUN' 
_em_imaging.illumination_mode               'FLOOD BEAM' 
_em_imaging.microscope_model                'FEI TITAN KRIOS' 
_em_imaging.mode                            'BRIGHT FIELD' 
_em_imaging.nominal_cs                      ? 
_em_imaging.nominal_defocus_max             ? 
_em_imaging.nominal_defocus_min             ? 
_em_imaging.nominal_magnification           ? 
_em_imaging.recording_temperature_maximum   ? 
_em_imaging.recording_temperature_minimum   ? 
_em_imaging.residual_tilt                   ? 
_em_imaging.specimen_holder_model           ? 
_em_imaging.specimen_id                     1 
_em_imaging.sample_support_id               1 
_em_imaging.citation_id                     ? 
_em_imaging.detector_id                     1 
_em_imaging.scans_id                        1 
_em_imaging.date                            ? 
_em_imaging.temperature                     ? 
_em_imaging.tilt_angle_min                  ? 
_em_imaging.tilt_angle_max                  ? 
_em_imaging.astigmatism                     ? 
_em_imaging.detector_distance               ? 
_em_imaging.electron_beam_tilt_params       ? 
_em_imaging.specimen_holder_type            ? 
_em_imaging.microscope_id                   ? 
# 
_em_sample_support.id               1 
_em_sample_support.specimen_id      1 
_em_sample_support.method           ? 
_em_sample_support.film_material    ? 
_em_sample_support.grid_material    ? 
_em_sample_support.grid_mesh_size   ? 
_em_sample_support.grid_type        ? 
_em_sample_support.details          ? 
# 
_em_vitrification.id                      1 
_em_vitrification.specimen_id             1 
_em_vitrification.chamber_temperature     295.2 
_em_vitrification.cryogen_name            ETHANE 
_em_vitrification.details                 'Blot for 4.5 seconds after 30 seconds of incubation.' 
_em_vitrification.humidity                100 
_em_vitrification.instrument              'FEI VITROBOT MARK IV' 
_em_vitrification.entry_id                EMD-0089 
_em_vitrification.sample_preparation_id   ? 
_em_vitrification.citation_id             ? 
_em_vitrification.method                  ? 
_em_vitrification.temp                    ? 
_em_vitrification.time_resolved_state     ? 
# 
_em_experiment.entry_id                EMD-0089 
_em_experiment.id                      1 
_em_experiment.aggregation_state       PARTICLE 
_em_experiment.reconstruction_method   'SINGLE PARTICLE' 
_em_experiment.entity_assembly_id      1 
# 
_em_single_particle_entity.entry_id              EMD-0089 
_em_single_particle_entity.id                    1 
_em_single_particle_entity.image_processing_id   1 
_em_single_particle_entity.point_symmetry        C14 
# 
_em_admin.entry_id              EMD-0089 
_em_admin.current_status        REL 
_em_admin.deposition_date       2018-06-28 
_em_admin.deposition_site       PDBE 
_em_admin.details               ? 
_em_admin.last_update           2024-11-06 
_em_admin.map_release_date      2018-10-24 
_em_admin.obsoleted_date        ? 
_em_admin.title                 
'Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri' 
_em_admin.header_release_date   2018-08-22 
# 
loop_
_em_author_list.ordinal 
_em_author_list.author 
1 'Costa, T.R.D.' 
2 'Sgro, G.G.'    
3 'Farah, C.S.'   
4 'Waksman, G.'   
# 
loop_
_em_buffer_component.buffer_id 
_em_buffer_component.id 
_em_buffer_component.concentration 
_em_buffer_component.concentration_units 
_em_buffer_component.formula 
_em_buffer_component.name 
1 1 20  mM 'NH2C(CH2OH)3HCl'      Tris-HCl          
1 2 200 mM NaCl                   'Sodium Chloride' 
1 3 10  mM 'CH3(CH2)11N(O)(CH3)2' LDAO              
# 
_em_ctf_correction.id                                1 
_em_ctf_correction.em_image_processing_id            1 
_em_ctf_correction.type                              'PHASE FLIPPING AND AMPLITUDE CORRECTION' 
_em_ctf_correction.details                           ? 
_em_ctf_correction.amplitude_correction              ? 
_em_ctf_correction.amplitude_correction_factor       ? 
_em_ctf_correction.amplitude_correction_space        ? 
_em_ctf_correction.correction_operation              ? 
_em_ctf_correction.phase_reversal                    ? 
_em_ctf_correction.phase_reversal_anisotropic        ? 
_em_ctf_correction.phase_reversal_correction_space   ? 
# 
_em_db_reference.id             1 
_em_db_reference.access_code    6GYB 
_em_db_reference.db_name        PDB 
_em_db_reference.details        ? 
_em_db_reference.relationship   'IN FRAME' 
# 
_em_entity_assembly_molwt.entity_assembly_id   1 
_em_entity_assembly_molwt.id                   1 
_em_entity_assembly_molwt.experimental_flag    NO 
_em_entity_assembly_molwt.units                ? 
_em_entity_assembly_molwt.value                ? 
# 
_em_entity_assembly_naturalsource.id                   2 
_em_entity_assembly_naturalsource.entity_assembly_id   1 
_em_entity_assembly_naturalsource.cell                 ? 
_em_entity_assembly_naturalsource.cellular_location    ? 
_em_entity_assembly_naturalsource.ncbi_tax_id          190486 
_em_entity_assembly_naturalsource.organ                ? 
_em_entity_assembly_naturalsource.organelle            ? 
_em_entity_assembly_naturalsource.organism             'Xanthomonas axonopodis pv. citri str. 306' 
_em_entity_assembly_naturalsource.strain               ? 
_em_entity_assembly_naturalsource.tissue               ? 
# 
_em_entity_assembly_recombinant.id                   2 
_em_entity_assembly_recombinant.entity_assembly_id   1 
_em_entity_assembly_recombinant.cell                 ? 
_em_entity_assembly_recombinant.ncbi_tax_id          469008 
_em_entity_assembly_recombinant.organism             'Escherichia coli BL21(DE3)' 
_em_entity_assembly_recombinant.plasmid              ? 
_em_entity_assembly_recombinant.strain               ? 
# 
loop_
_em_euler_angle_assignment.id 
_em_euler_angle_assignment.details 
_em_euler_angle_assignment.image_processing_id 
_em_euler_angle_assignment.order 
_em_euler_angle_assignment.proj_matching_angular_sampling 
_em_euler_angle_assignment.proj_matching_merit_function 
_em_euler_angle_assignment.proj_matching_num_projections 
_em_euler_angle_assignment.type 
1 ? 1 INITIAL ? ? ? 'MAXIMUM LIKELIHOOD' 
2 ? 1 FINAL   ? ? ? 'MAXIMUM LIKELIHOOD' 
# 
_em_final_classification.id                         1 
_em_final_classification.type                       3D 
_em_final_classification.avg_num_images_per_class   142306 
_em_final_classification.details                    ? 
_em_final_classification.image_processing_id        1 
_em_final_classification.num_classes                1 
# 
_em_grid_pretreatment.id                  1 
_em_grid_pretreatment.sample_support_id   1 
_em_grid_pretreatment.atmosphere          Air 
_em_grid_pretreatment.pressure            37 
_em_grid_pretreatment.time                25 
_em_grid_pretreatment.type                'GLOW DISCHARGE' 
# 
_em_image_processing.id                   1 
_em_image_processing.image_recording_id   1 
_em_image_processing.details              ? 
# 
_em_image_recording.id                            1 
_em_image_recording.imaging_id                    1 
_em_image_recording.avg_electron_dose_per_image   60 
_em_image_recording.average_exposure_time         12 
_em_image_recording.details                       ? 
_em_image_recording.detector_mode                 SUPER-RESOLUTION 
_em_image_recording.film_or_detector_model        'GATAN K2 QUANTUM (4k x 4k)' 
_em_image_recording.num_diffraction_images        ? 
_em_image_recording.num_grids_imaged              1 
_em_image_recording.num_real_images               1469 
# 
_em_map.entry_id               EMD-0089 
_em_map.id                     1 
_em_map.annotation_details     ? 
_em_map.axis_order_fast        X 
_em_map.axis_order_medium      Y 
_em_map.axis_order_slow        Z 
_em_map.cell_a                 370.99997 
_em_map.cell_alpha             90.0 
_em_map.cell_b                 370.99997 
_em_map.cell_beta              90.0 
_em_map.cell_c                 370.99997 
_em_map.cell_gamma             90.0 
_em_map.contour_level          0.035 
_em_map.contour_level_source   author 
_em_map.data_type              'Image stored as floating point number (4 bytes)' 
_em_map.dimensions_col         350 
_em_map.dimensions_row         350 
_em_map.dimensions_sec         350 
_em_map.endian_type            big 
_em_map.file                   emd_0089.map.gz 
_em_map.format                 CCP4 
_em_map.label                  ::::EMDATABANK.org::::EMD-0089:::: 
_em_map.limit_col              349 
_em_map.limit_row              349 
_em_map.limit_sec              349 
_em_map.origin_col             0 
_em_map.origin_row             0 
_em_map.origin_sec             0 
_em_map.partition              1 
_em_map.pixel_spacing_x        1.06 
_em_map.pixel_spacing_y        1.06 
_em_map.pixel_spacing_z        1.06 
_em_map.size_kb                171501024 
_em_map.spacing_x              350 
_em_map.spacing_y              350 
_em_map.spacing_z              350 
_em_map.statistics_average     6.112758E-4 
_em_map.statistics_maximum     0.27459824 
_em_map.statistics_minimum     -0.16240412 
_em_map.statistics_std         0.008838454 
_em_map.symmetry_space_group   1 
_em_map.type                   'primary map' 
# 
_em_particle_selection.id                       1 
_em_particle_selection.image_processing_id      1 
_em_particle_selection.details                  ? 
_em_particle_selection.method                   ? 
_em_particle_selection.num_particles_selected   185079 
_em_particle_selection.reference_model          ? 
# 
loop_
_em_software.id 
_em_software.category 
_em_software.details 
_em_software.name 
_em_software.version 
_em_software.image_processing_id 
_em_software.fitting_id 
_em_software.imaging_id 
1  'PARTICLE SELECTION'       ? RELION         2.0   1 ? ? 
2  'IMAGE ACQUISITION'        ? EPU            1.8   ? ? 1 
3  MASKING                    ? ?              ?     ? ? ? 
4  'CTF CORRECTION'           ? Gctf           1.06  1 ? ? 
5  'LAYERLINE INDEXING'       ? ?              ?     ? ? ? 
6  'DIFFRACTION INDEXING'     ? ?              ?     ? ? ? 
7  'MODEL FITTING'            ? Coot           0.8.6 ? 1 ? 
8  'MODEL FITTING'            ? 'UCSF Chimera' 8.6.1 ? 1 ? 
9  OTHER                      ? ?              ?     ? ? ? 
10 'INITIAL EULER ASSIGNMENT' ? cryoSPARC      1.0   1 ? ? 
11 'FINAL EULER ASSIGNMENT'   ? RELION         2.0   1 ? ? 
12 CLASSIFICATION             ? RELION         2.0   1 ? ? 
13 RECONSTRUCTION             ? RELION         2.0   1 ? ? 
14 'MODEL REFINEMENT'         ? PHENIX         1.12  ? 1 ? 
# 
_em_specimen.id                      1 
_em_specimen.experiment_id           1 
_em_specimen.concentration           0.3 
_em_specimen.details                 ? 
_em_specimen.embedding_applied       NO 
_em_specimen.shadowing_applied       NO 
_em_specimen.staining_applied        NO 
_em_specimen.vitrification_applied   YES 
# 
_em_start_model.id                               1 
_em_start_model.details                          ? 
_em_start_model.image_processing_id              1 
_em_start_model.emdb_id                          ? 
_em_start_model.insilico_model                   ? 
_em_start_model.orthogonal_tilt_angle1           ? 
_em_start_model.orthogonal_tilt_angle2           ? 
_em_start_model.orthogonal_tilt_num_images       ? 
_em_start_model.other                            ? 
_em_start_model.pdb_id                           ? 
_em_start_model.random_conical_tilt_angle        ? 
_em_start_model.random_conical_tilt_num_images   ? 
_em_start_model.type                             NONE 
# 
_em_support_film.id                  1 
_em_support_film.sample_support_id   1 
_em_support_film.material            CARBON 
_em_support_film.thickness           30 
_em_support_film.topology            LACEY 
# 
loop_
_pdbx_audit_support.funding_organization 
_pdbx_audit_support.country 
_pdbx_audit_support.grant_number 
_pdbx_audit_support.details 
_pdbx_audit_support.ordinal 
'Wellcome Trust'                'United Kingdom' 098302       ? 1 
'Sao Paulo Research Foundation' Brazil           2011/07777-5 ? 2 
'Sao Paulo Research Foundation' Brazil           2017/17303-7 ? 3 
# 
