data_7RVE

_audit_conform.dict_name      mmcif_pdbx_vrpt.dic
_audit_conform.dict_version   0.068
_audit_conform.dict_location  https://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx_vrpt.dic
#
_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7RVE
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   "electron crystallography"
#
_pdbx_vrpt_summary.entry_id                    7RVE
_pdbx_vrpt_summary.PDB_deposition_date         2021-08-18
_pdbx_vrpt_summary.PDB_revision_number         2
_pdbx_vrpt_summary.PDB_revision_date           2024-05-22
_pdbx_vrpt_summary.report_creation_date        2025-02-20:13:34
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds_mogul,validation_schema,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer  "Major prion protein"  
2  water    water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  pdb  
2  all  "electron microscopy"  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
4  RSRZ_outliers_percent         
5  R_value_R_free                
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
 1  1  1   99.96  210492  ?     ?     
 2  2  1   99.83   15764  ?     ?     
 3  1  2  100.00  207382  ?     ?     
 4  2  2  100.00   16835  ?     ?     
 5  1  3  100.00  206894  ?     ?     
 6  2  3  100.00   16415  ?     ?     
 7  1  4  100.00  164674  ?     ?     
 8  2  4  100.00      54  ?     ?     
 9  1  5   12.89  164678  ?     ?     
10  2  5   72.34      53  ?     ?     
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
3  5  3  A  1  1  A  100.00  
4  6  3  A  1  1  A  100.00  
5  7  4  A  1  1  A  100.00  
6  8  4  A  1  1  A  100.00  
#
_pdbx_vrpt_summary_entity_geometry.ordinal          1
_pdbx_vrpt_summary_entity_geometry.PDB_model_num    1
_pdbx_vrpt_summary_entity_geometry.entity_id        1
_pdbx_vrpt_summary_entity_geometry.label_asym_id    A
_pdbx_vrpt_summary_entity_geometry.auth_asym_id     A
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ      0.57
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.69
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   82
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  109
#
_pdbx_vrpt_summary_geometry.ordinal                        1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers       0.00
_pdbx_vrpt_summary_geometry.clashscore                     0.00
_pdbx_vrpt_summary_geometry.num_H_reduce                   64
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 82
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.69
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                109
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.57
#
_pdbx_vrpt_summary_diffraction.exp_method                "electron crystallography"
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            61.736
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         5.295
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.12(0.85A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        4694
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.522
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.503
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.331
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.948
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-l:0.305
_pdbx_vrpt_summary_diffraction.DCC_R                     0.2295
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.2804
_pdbx_vrpt_summary_diffraction.EDS_R                     0.2256
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.85
_pdbx_vrpt_summary_diffraction.EDS_res_low               9.86
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[6.165,4.747,5.158,0.062,-0.138,-0.277]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.265
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 36.28 % of the origin peak, indicating pseudo-translational symmetry.  The chance of finding a peak of this or larger height by random in a structure without pseudo-translational symmetry is equal to 5.1196e-04. The detected translational NCS is most likely also responsible for the elevated intensity ratio.  See the relevant section of the logfile for more details."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         2
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         90.60
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      423
_pdbx_vrpt_summary_diffraction.percent_free_reflections  9.02
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.density_fitness_version   1.0.11
_pdbx_vrpt_summary_diffraction.CCP4_version              "9.0.004 (Gargrove)"
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
 1  1  1  A  1  GLU  A  168  .  ?     
 2  1  1  A  2  TYR  A  169  .  ?     
 3  1  1  A  3  ASN  A  170  .  ?     
 4  1  1  A  4  ASN  A  171  .  ?     
 5  1  1  A  5  GLN  A  172  .  ?     
 6  1  1  A  6  ASN  A  173  .  ?     
 7  1  1  A  7  ASN  A  174  .  ?     
 8  1  1  A  8  PHE  A  175  .  ?     
 9  1  1  A  9  VAL  A  176  .  ?     
10  1  2  B  .  HOH  A  201  .  ?     
11  1  2  B  .  HOH  A  202  .  ?     
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.OWAB
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
_pdbx_vrpt_model_instance_geometry.average_occupancy
 1   1  tt0        ?      ?  ?           5  40.860     9  0.39    12  0.71  molprobity  1.000  
 2   2  t80   -114.2  116.6  Favored     9  11.520    13  1.16    18  0.90  molprobity  1.000  
 3   3  m-20  -120.8  123.0  Favored     6  16.290     8  0.44    11  0.43  molprobity  1.000  
 4   4  t30   -141.4  136.3  Favored     6  14.110     8  0.93    11  0.36  molprobity  1.000  
 5   5  tm0?  -154.6  135.4  Favored     8  26.760     9  0.61    12  0.48  molprobity  1.000  
 6   6  m-80  -143.8  142.9  Favored     6  16.640     8  0.54    11  0.52  molprobity  1.000  
 7   7  m-20  -123.5  128.5  Favored     6  15.230     8  0.64    11  0.57  molprobity  1.000  
 8   8  m-85  -122.9  112.8  Favored     9  17.340    12  0.43    16  0.26  molprobity  1.000  
 9   9  t          ?      ?  ?           9  51.980     7  0.26     7  0.37  molprobity  1.000  
10  10  ?          ?      ?  ?           ?  19.500     ?     ?     ?     ?  ?           1.000  
11  11  ?          ?      ?  ?           ?  25.040     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_model_instance_density.ordinal
_pdbx_vrpt_model_instance_density.instance_id
_pdbx_vrpt_model_instance_density.natoms_eds
_pdbx_vrpt_model_instance_density.RSRCC
_pdbx_vrpt_model_instance_density.RSR
_pdbx_vrpt_model_instance_density.RSRZ
_pdbx_vrpt_model_instance_density.EDIAm
_pdbx_vrpt_model_instance_density.OPIA
 1   1  17  0.985  0.055  -0.505  0.108   44.440  
 2   2  21  0.990  0.028  -0.921  0.936  100.000  
 3   3  14  0.985  0.034  -0.715  0.972  100.000  
 4   4  14  0.990  0.032  -0.778  0.861   87.500  
 5   5  17  0.993  0.027  -0.995  0.866   77.780  
 6   6  14  0.985  0.036  -0.652  0.856   75.000  
 7   7  14  0.986  0.037  -0.620  0.916  100.000  
 8   8  20  0.986  0.038  -0.448  0.988  100.000  
 9   9  17  0.951  0.092   1.910  0.141   28.570  
10  10   1  0.986  0.039       ?  0.734    0.000  
11  11   1  0.968  0.081       ?  0.498    0.000  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  eds          3.0                                                                   Y  
3  dcc          '"2.29  (2024-07-11))"'                                               Y  
4  xtriage      1.21                                                                  Y  
5  percentiles  "20231227.v01 (using entries in the PDB archive December 27th 2023)"  Y  
##
