data_1A3I

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1A3I
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    1A3I
_pdbx_vrpt_summary.PDB_deposition_date         1998-01-22
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2024-04-03
_pdbx_vrpt_summary.report_creation_date        2024-03-23:16:48
_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      "COLLAGEN-LIKE PEPTIDE"  
2  polymer      "COLLAGEN-LIKE PEPTIDE"  
3  non-polymer  "ACETIC ACID"  
4  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  2  
C  2  
D  3  
E  3  
F  4  
G  4  
H  4  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  1.97  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         
#
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   37.49  141614     ?     ?  
2  2  1   21.89    1014  1.98  1.98  
3  1  2  100.00  138981     ?     ?  
4  2  2  100.00    1006  1.98  1.98  
5  1  3  100.00  138945     ?     ?  
6  2  3  100.00    1006  1.98  1.98  
7  1  4  100.00  127900     ?     ?  
8  2  4  100.00   11410  1.96  2.00  
#
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  2  B  100.00  
 8  4  2  B  1  2  B  100.00  
 9  5  3  B  1  2  B  100.00  
10  6  3  B  1  2  B  100.00  
11  7  4  B  1  2  B  100.00  
12  8  4  B  1  2  B  100.00  
13  3  2  C  1  2  C  100.00  
14  4  2  C  1  2  C  100.00  
15  5  3  C  1  2  C  100.00  
16  6  3  C  1  2  C  100.00  
17  7  4  C  1  2  C  100.00  
18  8  4  C  1  2  C  100.00  
#
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  0.84  0.51  59  83  
2  1  2  B  B  0.69  0.72  39  54  
3  1  2  C  C  0.73  0.70  39  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                     7.66
_pdbx_vrpt_summary_geometry.num_H_reduce                   127
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                 137
_pdbx_vrpt_summary_geometry.bonds_RMSZ                     0.64
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                191
_pdbx_vrpt_summary_geometry.angles_RMSZ                    0.77
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            25.453
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         14.996
_pdbx_vrpt_summary_diffraction.I_over_sigma              3.74(1.97A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        1136
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.169
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.467
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.333
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.947
_pdbx_vrpt_summary_diffraction.twin_fraction             k,h,-l:0.170
_pdbx_vrpt_summary_diffraction.DCC_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_R                     0.20
_pdbx_vrpt_summary_diffraction.EDS_res_high              1.97
_pdbx_vrpt_summary_diffraction.EDS_res_low               26.82
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[12.988,12.409,22.054,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.610
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The analyses of the Patterson function reveals a significant off-origin peak that is 33.76 % 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 7.6013e-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         0
_pdbx_vrpt_summary_diffraction.centric_outliers          1
_pdbx_vrpt_summary_diffraction.data_completeness         88.51
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      0
_pdbx_vrpt_summary_diffraction.percent_free_reflections  0.00
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       1.97
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        8.00
_pdbx_vrpt_summary_diffraction.PDB_R                     0.18
#
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  PRO  A    1  .  ?        ?  
 2  1  1  A  2  PRO  A    2  .  ?        ?  
 3  1  1  A  3  GLY  A    3  .  ?        ?  
 4  1  1  A  4  PRO  A    4  .  ?        ?  
 5  1  1  A  5  PRO  A    5  .  ?        ?  
 6  1  1  A  6  GLY  A    6  .  ?        ?  
 7  1  1  A  7  PRO  A    7  .  ?        1  
 8  1  1  A  8  PRO  A    8  .  ?        ?  
 9  1  1  A  9  GLY  A    9  .  ?        ?  
10  1  2  B  1  PRO  B   31  .  ?        ?  
11  1  2  B  2  PRO  B   32  .  ?        ?  
12  1  2  B  3  GLY  B   33  .  ?        ?  
13  1  2  B  4  PRO  B   34  .  ?        ?  
14  1  2  B  5  PRO  B   35  .  ?        ?  
15  1  2  B  6  GLY  B   36  .  ?        ?  
16  1  2  C  1  PRO  C   61  .  ?        ?  
17  1  2  C  2  PRO  C   62  .  ?        ?  
18  1  2  C  3  GLY  C   63  .  ?        ?  
19  1  2  C  4  PRO  C   64  .  ?        ?  
20  1  2  C  5  PRO  C   65  .  ?        1  
21  1  2  C  6  GLY  C   66  .  ?        ?  
22  1  3  D  .  ACY  A  401  .  ?        1  
23  1  3  E  .  ACY  C  402  .  ?        ?  
24  1  4  F  .  HOH  A  101  .  ?        ?  
25  1  4  F  .  HOH  A  102  .  ?        ?  
26  1  4  F  .  HOH  A  103  .  ?        1  
27  1  4  F  .  HOH  A  104  .  ?        ?  
28  1  4  F  .  HOH  A  105  .  ?        ?  
29  1  4  F  .  HOH  A  106  .  ?        ?  
30  1  4  F  .  HOH  A  107  .  ?        ?  
31  1  4  F  .  HOH  A  108  .  ?        ?  
32  1  4  F  .  HOH  A  109  .  ?        ?  
33  1  4  F  .  HOH  A  201  .  ?        ?  
34  1  4  F  .  HOH  A  204  .  ?        ?  
35  1  4  F  .  HOH  A  209  .  ?        ?  
36  1  4  F  .  HOH  A  218  .  ?        ?  
37  1  4  F  .  HOH  A  220  .  ?        ?  
38  1  4  F  .  HOH  A  241  .  ?        ?  
39  1  4  F  .  HOH  A  244  .  ?        ?  
40  1  4  F  .  HOH  A  245  .  ?        ?  
41  1  4  G  .  HOH  B  111  .  ?        ?  
42  1  4  G  .  HOH  B  112  .  ?        ?  
43  1  4  G  .  HOH  B  113  .  ?        ?  
44  1  4  G  .  HOH  B  115  .  ?        ?  
45  1  4  G  .  HOH  B  116  .  ?        ?  
46  1  4  G  .  HOH  B  242  .  ?        ?  
47  1  4  G  .  HOH  B  246  .  ?        ?  
48  1  4  G  .  HOH  B  247  .  ?        ?  
49  1  4  H  .  HOH  C  121  .  ?        ?  
50  1  4  H  .  HOH  C  122  .  ?        ?  
51  1  4  H  .  HOH  C  123  .  ?        ?  
52  1  4  H  .  HOH  C  124  .  ?        ?  
53  1  4  H  .  HOH  C  125  .  ?        ?  
54  1  4  H  .  HOH  C  126  .  ?        ?  
55  1  4  H  .  HOH  C  202  .  ?        ?  
56  1  4  H  .  HOH  C  205  .  ?        ?  
57  1  4  H  .  HOH  C  208  .  ?        ?  
58  1  4  H  .  HOH  C  210  .  ?        ?  
59  1  4  H  .  HOH  C  243  .  ?        ?  
60  1  4  H  .  HOH  C  248  .  ?        ?  
#
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  Cg_endo      ?       ?  ?           9  19.510     8  0.24    12  1.03  molprobity  1.000  
 2   2  Cg_exo   -56.4   171.5  Allowed     7  15.530     8  0.42    11  0.64  molprobity  1.000  
 3   3  ?        -89.9   176.5  Favored     3  12.070     4  0.71     6  1.36  molprobity  1.000  
 4   4  Cg_endo  -79.1   163.7  Favored     7  11.820     8  0.56    12  0.74  molprobity  1.000  
 5   5  Cg_exo   -47.1   164.3  Allowed     7  12.690     8  0.35    11  0.62  molprobity  1.000  
 6   6  ?        -98.3   174.8  Favored     3  10.800     4  0.88     6  0.80  molprobity  1.000  
 7   7  Cg_endo  -60.6   160.6  Favored     7  11.150     8  0.59    12  0.84  molprobity  1.000  
 8   8  Cg_exo   -70.2   178.1  Favored     7  15.090     8  0.33    11  0.83  molprobity  1.000  
 9   9  ?            ?       ?  ?           3  11.650     3  0.69     2  0.42  molprobity  1.000  
10  10  Cg_endo      ?       ?  ?           7  11.570     8  0.56    12  0.37  molprobity  1.000  
11  11  Cg_exo   -58.9   150.0  Favored     7  11.680     8  0.80    11  0.90  molprobity  1.000  
12  12  ?        -73.0  -172.1  Favored     3  14.260     4  0.59     6  0.69  molprobity  1.000  
13  13  Cg_endo  -79.3   156.6  Favored     7  10.710     8  0.93    12  0.80  molprobity  1.000  
14  14  Cg_exo   -55.4   157.4  Favored     7  13.950     8  0.72    11  0.55  molprobity  1.000  
15  15  ?            ?       ?  ?           3  19.340     3  0.35     2  0.81  molprobity  1.000  
16  16  Cg_endo      ?       ?  ?           7  14.390     8  0.21    12  0.71  molprobity  1.000  
17  17  Cg_exo   -54.8   141.8  Favored     7  13.230     8  0.82    11  0.75  molprobity  1.000  
18  18  ?        -66.9   179.7  Favored     3  16.500     4  0.74     6  0.44  molprobity  1.000  
19  19  Cg_endo  -73.5   161.3  Favored     7  11.290     8  0.39    12  0.94  molprobity  1.000  
20  20  Cg_endo  -68.5   164.2  Favored     7  10.950     8  1.10    11  0.60  molprobity  1.000  
21  21  ?            ?       ?  ?           3   9.960     3  0.41     2  0.59  molprobity  1.000  
22  22  ?            ?       ?  ?           3  21.190     3  0.65     3  0.51  mogul       1.000  
23  23  ?            ?       ?  ?           3  38.320     3  0.72     3  0.23  mogul       1.000  
24  24  ?            ?       ?  ?           ?  28.970     ?     ?     ?     ?  ?           1.000  
25  25  ?            ?       ?  ?           ?  22.470     ?     ?     ?     ?  ?           1.000  
26  26  ?            ?       ?  ?           ?  29.020     ?     ?     ?     ?  ?           1.000  
27  27  ?            ?       ?  ?           ?  30.440     ?     ?     ?     ?  ?           1.000  
28  28  ?            ?       ?  ?           ?  23.320     ?     ?     ?     ?  ?           1.000  
29  29  ?            ?       ?  ?           ?   5.050     ?     ?     ?     ?  ?           1.000  
30  30  ?            ?       ?  ?           ?  21.020     ?     ?     ?     ?  ?           1.000  
31  31  ?            ?       ?  ?           ?  11.170     ?     ?     ?     ?  ?           1.000  
32  32  ?            ?       ?  ?           ?   9.230     ?     ?     ?     ?  ?           1.000  
33  33  ?            ?       ?  ?           ?  14.400     ?     ?     ?     ?  ?           1.000  
34  34  ?            ?       ?  ?           ?   7.430     ?     ?     ?     ?  ?           1.000  
35  35  ?            ?       ?  ?           ?  23.970     ?     ?     ?     ?  ?           1.000  
36  36  ?            ?       ?  ?           ?  17.320     ?     ?     ?     ?  ?           1.000  
37  37  ?            ?       ?  ?           ?  26.000     ?     ?     ?     ?  ?           1.000  
38  38  ?            ?       ?  ?           ?  16.810     ?     ?     ?     ?  ?           1.000  
39  39  ?            ?       ?  ?           ?  21.620     ?     ?     ?     ?  ?           1.000  
40  40  ?            ?       ?  ?           ?  23.050     ?     ?     ?     ?  ?           1.000  
41  41  ?            ?       ?  ?           ?  13.590     ?     ?     ?     ?  ?           1.000  
42  42  ?            ?       ?  ?           ?  27.990     ?     ?     ?     ?  ?           1.000  
43  43  ?            ?       ?  ?           ?  23.250     ?     ?     ?     ?  ?           1.000  
44  44  ?            ?       ?  ?           ?  24.120     ?     ?     ?     ?  ?           1.000  
45  45  ?            ?       ?  ?           ?  47.480     ?     ?     ?     ?  ?           1.000  
46  46  ?            ?       ?  ?           ?  23.110     ?     ?     ?     ?  ?           1.000  
47  47  ?            ?       ?  ?           ?  28.600     ?     ?     ?     ?  ?           1.000  
48  48  ?            ?       ?  ?           ?  26.870     ?     ?     ?     ?  ?           1.000  
49  49  ?            ?       ?  ?           ?  27.030     ?     ?     ?     ?  ?           1.000  
50  50  ?            ?       ?  ?           ?  25.940     ?     ?     ?     ?  ?           1.000  
51  51  ?            ?       ?  ?           ?  19.700     ?     ?     ?     ?  ?           1.000  
52  52  ?            ?       ?  ?           ?  31.730     ?     ?     ?     ?  ?           1.000  
53  53  ?            ?       ?  ?           ?  53.430     ?     ?     ?     ?  ?           1.000  
54  54  ?            ?       ?  ?           ?   9.430     ?     ?     ?     ?  ?           1.000  
55  55  ?            ?       ?  ?           ?  17.290     ?     ?     ?     ?  ?           1.000  
56  56  ?            ?       ?  ?           ?   7.900     ?     ?     ?     ?  ?           1.000  
57  57  ?            ?       ?  ?           ?  22.050     ?     ?     ?     ?  ?           1.000  
58  58  ?            ?       ?  ?           ?  20.070     ?     ?     ?     ?  ?           1.000  
59  59  ?            ?       ?  ?           ?  13.400     ?     ?     ?     ?  ?           1.000  
60  60  ?            ?       ?  ?           ?  22.690     ?     ?     ?     ?  ?           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   7  HG2  1  0.58  1.85  
2  20  HB3  1  0.58  1.85  
3  22  H1   2  0.78  1.82  
4  26  O    2  0.78  1.82  
#
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  7  0.899  0.121   0.294  
 2   2  7  0.919  0.136   0.575  
 3   3  4  0.956  0.089  -0.234  
 4   4  7  0.928  0.126   0.388  
 5   5  7  0.920  0.114   0.163  
 6   6  4  0.951  0.101  -0.020  
 7   7  7  0.939  0.095  -0.193  
 8   8  7  0.895  0.146   0.762  
 9   9  4  0.952  0.099  -0.055  
10  10  7  0.944  0.113   0.144  
11  11  7  0.967  0.079  -0.493  
12  12  4  0.942  0.110   0.141  
13  13  7  0.951  0.097  -0.155  
14  14  7  0.926  0.112   0.125  
15  15  4  0.885  0.161   1.052  
16  16  7  0.932  0.111   0.107  
17  17  7  0.942  0.093  -0.230  
18  18  4  0.948  0.076  -0.466  
19  19  7  0.962  0.081  -0.455  
20  20  7  0.929  0.111   0.107  
21  21  4  0.940  0.123   0.373  
22  22  4  0.743  0.379       ?  
23  23  4  0.581  0.430       ?  
24  24  1  0.693  0.227       ?  
25  25  1  0.900  0.126       ?  
26  26  1  0.848  0.218       ?  
27  27  1  0.819  0.259       ?  
28  28  1  0.827  0.302       ?  
29  29  1  0.960  0.141       ?  
30  30  1  0.549  0.429       ?  
31  31  1  0.882  0.178       ?  
32  32  1  0.951  0.083       ?  
33  33  1  0.933  0.111       ?  
34  34  1  0.963  0.157       ?  
35  35  1  0.921  0.160       ?  
36  36  1  0.909  0.339       ?  
37  37  1  0.908  0.295       ?  
38  38  1  0.908  0.114       ?  
39  39  1  0.675  0.197       ?  
40  40  1  0.922  0.281       ?  
41  41  1  0.943  0.363       ?  
42  42  1  0.825  0.229       ?  
43  43  1  0.751  0.209       ?  
44  44  1  0.819  0.193       ?  
45  45  1  0.794  0.448       ?  
46  46  1  0.777  0.225       ?  
47  47  1  0.579  0.306       ?  
48  48  1  0.891  0.258       ?  
49  49  1  0.863  0.162       ?  
50  50  1  0.799  0.177       ?  
51  51  1  0.910  0.113       ?  
52  52  1  0.789  0.205       ?  
53  53  1  0.690  0.374       ?  
54  54  1  0.939  0.153       ?  
55  55  1  0.873  0.244       ?  
56  56  1  0.946  0.120       ?  
57  57  1  0.832  0.250       ?  
58  58  1  0.908  0.149       ?  
59  59  1  0.775  0.250       ?  
60  60  1  0.867  0.168       ?  
#
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          2.36.1                                                                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  
##
