data_7RVF

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7RVF
#
_pdbx_vrpt_summary.entry_id                    7RVF
_pdbx_vrpt_summary.PDB_deposition_date         2021-08-18
_pdbx_vrpt_summary.PDB_revision_number         1
_pdbx_vrpt_summary.PDB_revision_date           2022-08-24
_pdbx_vrpt_summary.report_creation_date        2022-12-12:14:30
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,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   99.94  158937  ?     ?     
 2  2  1   99.23    4297  ?     ?     
 3  1  2  100.00  154571  ?     ?     
 4  2  2  100.00    4023  ?     ?     
 5  1  3  100.00  154315  ?     ?     
 6  2  3  100.00    3826  ?     ?     
 7  1  4    5.00  127900  ?     ?     
 8  2  4   -1.00       0  ?     ?     
 9  1  5   46.99  130704  ?     ?     
10  2  5   -1.00       0  ?     ?     
#
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    5.00  
6  8  4  A  1  1  A    8.31  
#
_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      0.94
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.60
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   80
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  107
#
_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                   66
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 80
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.60
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                107
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.94
#
_pdbx_vrpt_summary_diffraction.exp_method                ?
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 400.000
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         6.666
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.09(1.00A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2938
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.837
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.473
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.296
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.947
_pdbx_vrpt_summary_diffraction.twin_fraction             h,-h-k,-h-l:0.206
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.22
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.00
_pdbx_vrpt_summary_diffraction.EDS_res_low               10.24
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[7.306,5.803,6.678,0.024,-0.064,0.102]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.228
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 66.08 % 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 6.4005e-06. 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         0
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         94.83
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      294
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.01
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     11.11
#
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  GLN  A  168  .  ?     
 2  1  1  A  2  PHE  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        ?      ?  ?           7  11.440     9  0.50    12  0.53  molprobity  1.000  
 2   2  t80   -104.6  114.6  Favored     9   5.750    12  0.54    16  1.40  molprobity  1.000  
 3   3  m-20  -116.7  119.5  Favored     6   6.060     8  0.76    11  0.68  molprobity  1.000  
 4   4  t30   -143.0  123.4  Favored     6   3.780     8  0.60    11  0.64  molprobity  1.000  
 5   5  tm0?  -143.2  132.7  Favored     8   2.820     9  0.77    12  0.98  molprobity  1.000  
 6   6  m-80  -141.9  138.5  Favored     6   3.300     8  0.42    11  1.02  molprobity  1.000  
 7   7  m-20  -116.5  128.3  Favored     6   3.570     8  0.65    11  0.81  molprobity  1.000  
 8   8  m-85  -121.4  106.7  Favored     9   5.700    12  0.42    16  0.97  molprobity  1.000  
 9   9  t          ?      ?  ?           9  14.600     6  0.72     7  0.75  molprobity  1.000  
10  10  ?          ?      ?  ?           ?  22.650     ?     ?     ?     ?  ?           1.000  
11  11  ?          ?      ?  ?           ?  19.830     ?     ?     ?     ?  ?           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
 1   1   9  0.857  0.112  0.601  
 2   2  11  0.931  0.097  0.980  
 3   3   8  0.932  0.102  0.621  
 4   4   8  0.952  0.095  0.460  
 5   5   9  0.965  0.087  0.074  
 6   6   8  0.924  0.132  1.310  
 7   7   8  0.943  0.113  0.874  
 8   8  11  0.901  0.111  1.448  
 9   9   7  0.751  0.229  5.356  
10  10   1  0.906  0.244      ?  
11  11   1  0.881  0.097      ?  
#
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          2.31.2                                                                Y  
3  dcc          "2.26  (2020-01-20)"                                                  Y  
4  xtriage      1.13                                                                  Y  
5  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
