data_1JXW

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1JXW
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1JXW
_pdbx_vrpt_summary.PDB_deposition_date         2001-09-10
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2023-08-16
_pdbx_vrpt_summary.report_creation_date        2023-08-06:13:18
_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      Crambin  
2  non-polymer  ETHANOL  
#
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   x-ray  
2  0.89  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      
#
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   42.15  141614     ?     ?  
2  2  1   34.36    1132  0.76  1.04  
3  1  2  100.00  138981     ?     ?  
4  2  2  100.00    1055  0.76  1.04  
5  1  3  100.00  138945     ?     ?  
6  2  3  100.00    1056  0.76  1.04  
#
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  
#
_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      1.10
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       1.14
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   470
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  637
#
_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                     6.86
_pdbx_vrpt_summary_geometry.num_H_reduce                   450
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 470
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     1.14
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                637
_pdbx_vrpt_summary_geometry.angles_RMSZ                    1.10
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 84.598
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            27.255
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         4.244
_pdbx_vrpt_summary_diffraction.I_over_sigma              1.87(0.89A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        26032
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.220
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.467
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.482
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.317
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.920
_pdbx_vrpt_summary_diffraction.twin_fraction             -h,-k,l:0.043
_pdbx_vrpt_summary_diffraction.DCC_R                     0.23
_pdbx_vrpt_summary_diffraction.EDS_R                     0.24
_pdbx_vrpt_summary_diffraction.EDS_res_high              0.89
_pdbx_vrpt_summary_diffraction.EDS_res_low               16.87
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[4.057,4.407,4.259,0.000,0.153,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.083
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 18.58% of the height of the origin peak. No significant pseudotranslation is detected."
_pdbx_vrpt_summary_diffraction.B_factor_type             FULL
_pdbx_vrpt_summary_diffraction.acentric_outliers         0
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         92.58
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      0
_pdbx_vrpt_summary_diffraction.percent_free_reflections  0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       0.89
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        17.67
_pdbx_vrpt_summary_diffraction.PDB_R                     0.14
#
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_bond_outliers
_pdbx_vrpt_model_instance.count_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  THR  A   1  .  ?        ?     ?     ?  
 2  1  1  A   2  THR  A   2  A  ?        ?     ?     ?  
 3  1  1  A   2  THR  A   2  B  ?        ?     ?     ?  
 4  1  1  A   3  CYS  A   3  .  ?        ?     ?     ?  
 5  1  1  A   4  CYS  A   4  .  ?        ?     ?     ?  
 6  1  1  A   5  PRO  A   5  .  ?        ?     ?     ?  
 7  1  1  A   6  SER  A   6  .  ?        ?     ?     ?  
 8  1  1  A   7  ILE  A   7  A  ?        ?     ?     ?  
 9  1  1  A   7  ILE  A   7  B  ?        ?     ?     ?  
10  1  1  A   8  VAL  A   8  A  ?        ?     ?     ?  
11  1  1  A   8  VAL  A   8  B  ?        ?     ?     ?  
12  1  1  A   8  VAL  A   8  C  ?        ?     ?     ?  
13  1  1  A   9  ALA  A   9  .  ?        ?     ?     ?  
14  1  1  A  10  ARG  A  10  A  ?        ?     ?     ?  
15  1  1  A  10  ARG  A  10  B  ?        ?     ?     ?  
16  1  1  A  11  SER  A  11  .  ?        ?     ?     ?  
17  1  1  A  12  ASN  A  12  A  ?        ?     ?     ?  
18  1  1  A  12  ASN  A  12  B  ?        ?     ?     ?  
19  1  1  A  13  PHE  A  13  A  ?        ?     ?     ?  
20  1  1  A  13  PHE  A  13  B  ?        ?     ?     ?  
21  1  1  A  14  ASN  A  14  .  ?        ?     ?     ?  
22  1  1  A  15  VAL  A  15  .  ?        ?     ?     ?  
23  1  1  A  16  CYS  A  16  .  ?        ?     ?     ?  
24  1  1  A  17  ARG  A  17  .  ?        ?     ?     ?  
25  1  1  A  18  LEU  A  18  .  ?        ?     ?     ?  
26  1  1  A  19  PRO  A  19  .  ?        ?     ?     ?  
27  1  1  A  20  GLY  A  20  .  ?        ?     ?     ?  
28  1  1  A  21  THR  A  21  .  ?        ?     ?     ?  
29  1  1  A  22  SER  A  22  B  ?        1     ?     ?  
30  1  1  A  22  SER  A  22  C  ?        1     ?     ?  
31  1  1  A  22  PRO  A  22  A  ?        ?     ?     ?  
32  1  1  A  23  GLU  A  23  A  ?        ?     ?     ?  
33  1  1  A  23  GLU  A  23  B  ?        ?     ?     ?  
34  1  1  A  24  ALA  A  24  .  ?        ?     ?     ?  
35  1  1  A  25  ILE  A  25  B  ?        ?     ?     ?  
36  1  1  A  25  ILE  A  25  C  ?        ?     ?     ?  
37  1  1  A  25  LEU  A  25  A  ?        1     ?     ?  
38  1  1  A  26  CYS  A  26  .  ?        ?     ?     ?  
39  1  1  A  27  ALA  A  27  .  ?        ?     ?     ?  
40  1  1  A  28  THR  A  28  .  ?        ?     ?     ?  
41  1  1  A  29  TYR  A  29  A  ?        ?     ?     ?  
42  1  1  A  29  TYR  A  29  B  ?        ?     ?     ?  
43  1  1  A  30  THR  A  30  A  ?        ?     ?     ?  
44  1  1  A  30  THR  A  30  B  ?        ?     ?     ?  
45  1  1  A  31  GLY  A  31  .  ?        ?     ?     ?  
46  1  1  A  32  CYS  A  32  .  ?        ?     ?     ?  
47  1  1  A  33  ILE  A  33  .  ?        ?     ?     ?  
48  1  1  A  34  ILE  A  34  A  ?        ?     ?     ?  
49  1  1  A  34  ILE  A  34  B  ?        ?     ?     ?  
50  1  1  A  35  ILE  A  35  .  ?        ?     ?     ?  
51  1  1  A  36  PRO  A  36  .  ?        ?     ?     ?  
52  1  1  A  37  GLY  A  37  .  ?        ?     ?     ?  
53  1  1  A  38  ALA  A  38  .  ?        ?     ?     ?  
54  1  1  A  39  THR  A  39  A  ?        ?     ?     ?  
55  1  1  A  39  THR  A  39  B  ?        ?     ?     3  
56  1  1  A  40  CYS  A  40  .  ?        ?     ?     1  
57  1  1  A  41  PRO  A  41  .  ?        ?     ?     ?  
58  1  1  A  42  GLY  A  42  .  ?        ?     ?     ?  
59  1  1  A  43  ASP  A  43  A  ?        ?     1     ?  
60  1  1  A  43  ASP  A  43  B  ?        ?     1     4  
61  1  1  A  44  TYR  A  44  .  ?        ?     ?     ?  
62  1  1  A  45  ALA  A  45  .  ?        ?     ?     ?  
63  1  1  A  46  ASN  A  46  .  ?        ?     ?     ?  
64  1  2  B   .  EOH  A  66  A  ?        ?     ?     ?  
65  1  2  B   .  EOH  A  66  B  ?        ?     ?     ?  
#
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.cis_peptide
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_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
 1   1  m             ?       ?  ?        ?      9   7  0.86  10  1.12  molprobity  
 2   2  p        -101.6   134.6  Favored  ?      7   7  0.48  10  1.06  molprobity  
 3   3  p        -101.6   134.6  Favored  ?      7   7  0.48  10  1.06  molprobity  
 4   4  m        -131.2   135.9  Favored  ?      4   6  0.68   8  0.71  molprobity  
 5   5  m        -122.3   147.6  Favored  ?      4   6  0.30   9  0.36  molprobity  
 6   6  Cg_endo   -75.1   -21.2  Favored  ?      7   8  0.71  11  0.72  molprobity  
 7   7  p        -155.6   167.5  Favored  ?      5   6  0.61   8  1.00  molprobity  
 8   8  mt        -57.5   -51.5  Favored  ?     11   8  0.44  11  1.17  molprobity  
 9   9  mt        -57.5   -51.5  Favored  ?     11   8  0.44  11  1.17  molprobity  
10  10  t         -64.1   -33.3  Favored  ?      9   7  0.54  10  1.95  molprobity  
11  11  t         -64.1   -33.3  Favored  ?      9   7  0.54  10  1.95  molprobity  
12  12  t         -64.1   -33.3  Favored  ?      9   7  0.54  10  1.95  molprobity  
13  13  ?         -60.6   -45.3  Favored  ?      5   5  0.32   7  0.99  molprobity  
14  14  tpp180    -60.2   -44.8  Favored  ?      9  11  0.34  14  1.02  molprobity  
15  15  tpp180    -60.2   -44.8  Favored  ?      9  11  0.34  14  1.02  molprobity  
16  16  m         -62.1   -41.3  Favored  ?      5   6  0.87   8  0.38  molprobity  
17  17  m-20      -77.3   -25.7  Favored  ?      6   8  0.31  11  0.57  molprobity  
18  18  m-20      -77.3   -25.7  Favored  ?      6   8  0.31  11  0.57  molprobity  
19  19  t80       -59.1   -46.5  Favored  ?      7  12  0.81  16  0.81  molprobity  
20  20  t80       -59.1   -46.5  Favored  ?      7  12  0.81  16  0.81  molprobity  
21  21  m-20      -65.0   -35.7  Favored  ?      6   8  0.50  11  0.69  molprobity  
22  22  t         -67.1   -43.9  Favored  ?      9   7  0.47  10  0.60  molprobity  
23  23  t         -53.2   -37.3  Favored  ?      4   6  0.55   8  0.78  molprobity  
24  24  mmm180    -74.5   -19.1  Favored  ?     13  11  0.35  14  1.02  molprobity  
25  25  mt        -55.3   -43.8  Favored  ?     11   8  0.68  12  0.88  molprobity  
26  26  Cg_endo   -76.1    -6.2  Favored  ?      7   8  0.79  11  0.64  molprobity  
27  27  ?         102.9    10.1  Favored  ?      3   4  0.83   5  0.66  molprobity  
28  28  m         -51.1   135.2  Favored  ?      7   7  0.24  10  0.70  molprobity  
29  29  p             ?       ?  ?        Y      5   5  5.75   5  1.93  molprobity  
30  30  p             ?       ?  ?        Y      5   5  5.75   5  1.93  molprobity  
31  31  Cg_exo        ?       ?  ?        Y      7   8  1.15  11  0.70  molprobity  
32  32  mt-10     -52.4   -39.3  Favored  ?      5   9  1.81  12  0.78  molprobity  
33  33  mt-10     -52.4   -39.3  Favored  ?      4   9  1.81  12  0.78  molprobity  
34  34  ?         -64.4   -37.1  Favored  ?      5   5  0.52   7  0.31  molprobity  
35  35  mm            ?       ?  ?        Y     11   7  0.48   8  0.68  molprobity  
36  36  mm            ?       ?  ?        Y     11   7  0.48   8  0.68  molprobity  
37  37  mt            ?       ?  ?        Y     10   8  2.17  11  1.81  molprobity  
38  38  m         -63.7   -30.5  Favored  ?      3   6  0.37   8  0.37  molprobity  
39  39  ?         -63.5   -52.9  Favored  ?      5   5  0.33   7  0.89  molprobity  
40  40  p         -68.0   -25.8  Favored  ?      7   7  0.75  10  0.70  molprobity  
41  41  t80       -68.2   -34.3  Favored  ?      7  13  0.53  18  0.92  molprobity  
42  42  t80       -68.2   -34.3  Favored  ?      7  13  0.53  18  0.92  molprobity  
43  43  p        -101.5   -30.7  Favored  ?      7   7  0.56  10  1.78  molprobity  
44  44  p        -101.5   -30.7  Favored  ?      7   7  0.56  10  1.78  molprobity  
45  45  ?          91.0    -2.3  Favored  ?      3   4  0.33   5  0.89  molprobity  
46  46  m         -67.3   167.9  Favored  ?      4   6  0.59   8  0.88  molprobity  
47  47  pt       -132.8   156.8  Favored  ?     11   8  0.31  11  0.78  molprobity  
48  48  mt       -113.2   127.4  Favored  ?      6   8  0.95  11  1.28  molprobity  
49  49  mt       -113.2   127.4  Favored  ?      6   8  0.95  11  1.28  molprobity  
50  50  pt       -124.3   157.2  Favored  ?     11   8  0.40  12  0.69  molprobity  
51  51  Cg_endo   -78.8   -26.6  Favored  ?      7   8  0.91  11  0.60  molprobity  
52  52  ?         -80.8  -174.4  Favored  ?      3   4  0.73   5  0.93  molprobity  
53  53  ?        -113.7     0.4  Favored  ?      5   5  0.43   7  1.05  molprobity  
54  54  m        -138.0   127.1  Favored  ?      7   7  0.79  10  1.70  molprobity  
55  55  m        -138.0   127.1  Favored  ?      7   7  0.79  10  1.70  molprobity  
56  56  m         -75.0   144.1  Favored  ?      4   6  0.49   9  0.52  molprobity  
57  57  Cg_endo   -77.8   165.5  Favored  ?      7   8  1.16  11  0.42  molprobity  
58  58  ?         -61.2   -23.4  Favored  ?      3   4  0.92   5  1.15  molprobity  
59  59  p-10      -93.2     2.6  Favored  ?      4   8  0.96  11  1.89  molprobity  
60  60  p-10      -93.2     2.6  Favored  ?      4   8  0.96  11  1.89  molprobity  
61  61  m-85     -133.7    60.3  Allowed  ?      9  13  0.49  18  0.95  molprobity  
62  62  ?         -88.3    -6.3  Favored  ?      5   5  0.56   7  1.20  molprobity  
63  63  m120          ?       ?  ?        ?      6   8  0.91   8  0.62  molprobity  
64  64  ?             ?       ?  ?        ?      6   2  0.55   1  0.15  mogul       
65  65  ?             ?       ?  ?        ?      6   2  0.58   1  0.08  mogul       
#
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  55  CA  1  1.37  1.90  
2  55  CA  2  0.80  2.45  
3  55  CB  3  0.54  2.57  
4  56  N   2  0.80  2.45  
5  60  CA  4  1.57  1.75  
6  60  CB  4  1.57  1.75  
7  60  CB  5  0.80  2.45  
8  60  CB  6  0.63  2.64  
#
loop_
_pdbx_vrpt_instance_intra_bond_outliers.ordinal
_pdbx_vrpt_instance_intra_bond_outliers.instance_id
_pdbx_vrpt_instance_intra_bond_outliers.atom_1
_pdbx_vrpt_instance_intra_bond_outliers.atom_2
_pdbx_vrpt_instance_intra_bond_outliers.obs
_pdbx_vrpt_instance_intra_bond_outliers.mean
_pdbx_vrpt_instance_intra_bond_outliers.stdev
_pdbx_vrpt_instance_intra_bond_outliers.Z
1  29  CB  OG   1.255  1.418  0.013  -12.57  
2  30  CB  OG   1.255  1.418  0.013  -12.57  
3  37  CG  CD2  1.728  1.514  0.037    5.79  
#
loop_
_pdbx_vrpt_instance_intra_angle_outliers.ordinal
_pdbx_vrpt_instance_intra_angle_outliers.instance_id
_pdbx_vrpt_instance_intra_angle_outliers.atom_1
_pdbx_vrpt_instance_intra_angle_outliers.atom_2
_pdbx_vrpt_instance_intra_angle_outliers.atom_3
_pdbx_vrpt_instance_intra_angle_outliers.obs
_pdbx_vrpt_instance_intra_angle_outliers.mean
_pdbx_vrpt_instance_intra_angle_outliers.stdev
_pdbx_vrpt_instance_intra_angle_outliers.Z
1  59  CB  CG  OD2  113.764  118.300  0.900  -5.04  
2  60  CB  CG  OD2  113.764  118.300  0.900  -5.04  
#
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          2.35                                                                  Y  
4  dcc          '"2.27  (2023-04-10)"'                                                Y  
5  xtriage      1.13                                                                  Y  
6  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
