data_3NHD

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  3NHD
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    3NHD
_pdbx_vrpt_summary.PDB_deposition_date         2010-06-14
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2022-12-21
_pdbx_vrpt_summary.report_creation_date        2022-12-11:06:50
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,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  non-polymer  "ACETIC ACID"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  1.92  x-ray  
#
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   24.11  141614     ?     ?  
 2  2  1   14.23    8644  1.90  1.94  
 3  1  2  100.00  138981     ?     ?  
 4  2  2  100.00    8530  1.90  1.94  
 5  1  3  100.00  138945     ?     ?  
 6  2  3  100.00    8530  1.90  1.94  
 7  1  4   10.97  127900     ?     ?  
 8  2  4   13.01    7793  1.90  1.94  
 9  1  5   46.99  130704     ?     ?  
10  2  5   35.18    7937  1.90  1.94  
#
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  
 7  3  2  B  1  1  B  100.00  
 8  4  2  B  1  1  B  100.00  
 9  5  3  B  1  1  B  100.00  
10  6  3  B  1  1  B  100.00  
11  7  4  B  1  1  B    1.22  
12  8  4  B  1  1  B    1.44  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.83  0.85  42  54  
2  1  1  B  B  0.75  0.84  42  54  
#
_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                     10.99
_pdbx_vrpt_summary_geometry.num_H_reduce                   90
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 84
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.84
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                108
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.79
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            122.330
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         13.837
_pdbx_vrpt_summary_diffraction.I_over_sigma              9.89(1.93A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        620
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.337
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.468
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.339
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.931
_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              1.92
_pdbx_vrpt_summary_diffraction.EDS_res_low               17.22
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[9.072,10.479,22.158,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.941
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 34.95 % 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 6.3007e-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         91.99
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      63
_pdbx_vrpt_summary_diffraction.percent_free_reflections  10.16
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     8.33
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.92
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        20.58
_pdbx_vrpt_summary_diffraction.PDB_R                     0.21
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.26
#
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
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A  1  GLY  A   1  .  ?        ?  
 2  1  1  A  2  TYR  A   2  .  ?        ?  
 3  1  1  A  3  VAL  A   3  .  ?        2  
 4  1  1  A  4  LEU  A   4  .  ?        ?  
 5  1  1  A  5  GLY  A   5  .  ?        ?  
 6  1  1  A  6  SER  A   6  .  ?        ?  
 7  1  1  B  1  GLY  B   1  .  ?        ?  
 8  1  1  B  2  TYR  B   2  .  ?        ?  
 9  1  1  B  3  VAL  B   3  .  ?        ?  
10  1  1  B  4  LEU  B   4  .  ?        2  
11  1  1  B  5  GLY  B   5  .  ?        ?  
12  1  1  B  6  SER  B   6  .  ?        ?  
13  1  2  C  .  ACY  A   7  .  ?        ?  
14  1  2  D  .  ACY  A   8  .  ?        ?  
15  1  3  E  .  HOH  A   9  .  ?        ?  
16  1  3  E  .  HOH  A  10  .  ?        ?  
#
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  ?          ?      ?  ?           5   7.850     4  1.21     5  0.44  molprobity  1.000  
 2   2  p90   -143.9  162.6  Favored     9   5.420    13  0.86    18  0.53  molprobity  1.000  
 3   3  t     -142.2  131.5  Favored     9   3.180     7  1.08    10  1.00  molprobity  1.000  
 4   4  mp    -113.4  122.5  Favored    11   8.050     8  0.59    11  1.25  molprobity  1.000  
 5   5  ?      -68.6  -36.0  Favored     3  11.510     4  0.69     5  0.52  molprobity  1.000  
 6   6  m          ?      ?  ?           5  15.360     6  0.51     5  0.75  molprobity  1.000  
 7   7  ?          ?      ?  ?           5  11.520     4  1.52     5  0.35  molprobity  1.000  
 8   8  p90    -59.3  158.4  Favored     9   9.370    13  0.79    18  0.71  molprobity  1.000  
 9   9  t     -133.8  120.0  Favored     9   8.010     7  1.10    10  0.71  molprobity  1.000  
10  10  mt    -109.2  135.7  Favored    11   6.200     8  0.49    11  0.76  molprobity  1.000  
11  11  ?     -135.3  132.3  Favored     3   8.880     4  0.42     5  0.38  molprobity  1.000  
12  12  t          ?      ?  ?           5  14.590     6  0.44     5  1.27  molprobity  1.000  
13  13  ?          ?      ?  ?           3  23.390     3  0.63     3  1.18  mogul       1.000  
14  14  ?          ?      ?  ?           3  31.420     3  0.82     3  0.73  mogul       1.000  
15  15  ?          ?      ?  ?           ?  20.230     ?     ?     ?     ?  ?           1.000  
16  16  ?          ?      ?  ?           ?  40.690     ?     ?     ?     ?  ?           1.000  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
1   3  HG13  1  0.70  1.73  
2   3  HG13  2  0.53  2.38  
3  10  HD23  1  0.70  1.73  
4  10  CD2   2  0.53  2.38  
#
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   4  0.885  0.138   0.641  
 2   2  12  0.916  0.122   0.438  
 3   3   7  0.965  0.079  -0.649  
 4   4   8  0.930  0.125   0.286  
 5   5   4  0.903  0.135   0.588  
 6   6   7  0.874  0.207   1.754  
 7   7   4  0.934  0.117   0.266  
 8   8  12  0.902  0.153   1.149  
 9   9   7  0.950  0.092  -0.360  
10  10   8  0.938  0.107  -0.116  
11  11   4  0.925  0.112   0.177  
12  12   7  0.681  0.244   2.418  
13  13   4  0.763  0.201       ?  
14  14   4  0.745  0.206       ?  
15  15   1  0.922  0.117       ?  
16  16   1  0.749  0.430       ?  
#
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  mogul        "1.8.5 (274361), CSD as541be (2020)"                                  Y  
3  eds          2.31.2                                                                Y  
4  dcc          "2.26  (2020-01-20)"                                                  Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
