data_1SDF

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1SDF
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    1SDF
_pdbx_vrpt_summary.PDB_deposition_date         1997-11-15
_pdbx_vrpt_summary.PDB_revision_number         4
_pdbx_vrpt_summary.PDB_revision_date           2022-03-02
_pdbx_vrpt_summary.report_creation_date        2022-08-21:11:48
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,coreclust,chemicalshifts,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
_pdbx_vrpt_entity.id           1
_pdbx_vrpt_entity.type         polymer
_pdbx_vrpt_entity.description  "STROMAL CELL-DERIVED FACTOR-1"
#
_pdbx_vrpt_asym.label_asym_id  A
_pdbx_vrpt_asym.entity_id      1
#
_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      0.82
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ       0.57
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ   561
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ  756
#
_pdbx_vrpt_summary_geometry.ordinal                                    1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers_full_length  9.23
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers_full_length       12.90
_pdbx_vrpt_summary_geometry.clashscore_full_length                     17.79
_pdbx_vrpt_summary_geometry.num_H_reduce                               574
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                             561
_pdbx_vrpt_summary_geometry.bonds_RMSZ                                 0.57
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                            756
_pdbx_vrpt_summary_geometry.angles_RMSZ                                0.82
#
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
_pdbx_vrpt_model_instance.count_plane_outliers
 1  1  1  A   1  LYS  A   1  .  ?        1     ?  
 2  1  1  A   2  PRO  A   2  .  ?        1     ?  
 3  1  1  A   3  VAL  A   3  .  ?        1     ?  
 4  1  1  A   4  SER  A   4  .  ?        1     ?  
 5  1  1  A   5  LEU  A   5  .  ?        ?     ?  
 6  1  1  A   6  SER  A   6  .  ?        ?     ?  
 7  1  1  A   7  TYR  A   7  .  ?        2     ?  
 8  1  1  A   8  ARG  A   8  .  ?        2     1  
 9  1  1  A   9  CYS  A   9  .  ?        ?     ?  
10  1  1  A  10  PRO  A  10  .  ?        1     ?  
11  1  1  A  11  CYS  A  11  .  ?        ?     ?  
12  1  1  A  12  ARG  A  12  .  ?        ?     1  
13  1  1  A  13  PHE  A  13  .  ?        ?     ?  
14  1  1  A  14  PHE  A  14  .  ?        ?     ?  
15  1  1  A  15  GLU  A  15  .  ?        1     ?  
16  1  1  A  16  SER  A  16  .  ?        1     ?  
17  1  1  A  17  HIS  A  17  .  ?        ?     ?  
18  1  1  A  18  VAL  A  18  .  ?        3     ?  
19  1  1  A  19  ALA  A  19  .  ?        2     ?  
20  1  1  A  20  ARG  A  20  .  ?        ?     1  
21  1  1  A  21  ALA  A  21  .  ?        ?     ?  
22  1  1  A  22  ASN  A  22  .  ?        ?     ?  
23  1  1  A  23  VAL  A  23  .  ?        2     ?  
24  1  1  A  24  LYS  A  24  .  ?        ?     ?  
25  1  1  A  25  HIS  A  25  .  ?        ?     ?  
26  1  1  A  26  LEU  A  26  .  ?        2     ?  
27  1  1  A  27  LYS  A  27  .  ?        1     ?  
28  1  1  A  28  ILE  A  28  .  ?        1     ?  
29  1  1  A  29  LEU  A  29  .  ?        ?     ?  
30  1  1  A  30  ASN  A  30  .  ?        ?     ?  
31  1  1  A  31  THR  A  31  .  ?        1     ?  
32  1  1  A  32  PRO  A  32  .  ?        1     ?  
33  1  1  A  33  ASN  A  33  .  ?        ?     ?  
34  1  1  A  34  CYS  A  34  .  ?        ?     ?  
35  1  1  A  35  ALA  A  35  .  ?        ?     ?  
36  1  1  A  36  LEU  A  36  .  ?        1     ?  
37  1  1  A  37  GLN  A  37  .  ?        1     ?  
38  1  1  A  38  ILE  A  38  .  ?        ?     ?  
39  1  1  A  39  VAL  A  39  .  ?        1     ?  
40  1  1  A  40  ALA  A  40  .  ?        ?     ?  
41  1  1  A  41  ARG  A  41  .  ?        ?     1  
42  1  1  A  42  LEU  A  42  .  ?        ?     ?  
43  1  1  A  43  LYS  A  43  .  ?        ?     ?  
44  1  1  A  44  ASN  A  44  .  ?        ?     ?  
45  1  1  A  45  ASN  A  45  .  ?        ?     ?  
46  1  1  A  46  ASN  A  46  .  ?        ?     ?  
47  1  1  A  47  ARG  A  47  .  ?        ?     1  
48  1  1  A  48  GLN  A  48  .  ?        ?     ?  
49  1  1  A  49  VAL  A  49  .  ?        ?     ?  
50  1  1  A  50  CYS  A  50  .  ?        ?     ?  
51  1  1  A  51  ILE  A  51  .  ?        5     ?  
52  1  1  A  52  ASP  A  52  .  ?        ?     ?  
53  1  1  A  53  PRO  A  53  .  ?        ?     ?  
54  1  1  A  54  LYS  A  54  .  ?        ?     ?  
55  1  1  A  55  LEU  A  55  .  ?        3     ?  
56  1  1  A  56  LYS  A  56  .  ?        ?     ?  
57  1  1  A  57  TRP  A  57  .  ?        ?     ?  
58  1  1  A  58  ILE  A  58  .  ?        2     ?  
59  1  1  A  59  GLN  A  59  .  ?        ?     ?  
60  1  1  A  60  GLU  A  60  .  ?        ?     ?  
61  1  1  A  61  TYR  A  61  .  ?        2     ?  
62  1  1  A  62  LEU  A  62  .  ?        ?     ?  
63  1  1  A  63  GLU  A  63  .  ?        ?     ?  
64  1  1  A  64  LYS  A  64  .  ?        ?     ?  
65  1  1  A  65  ALA  A  65  .  ?        1     ?  
66  1  1  A  66  LEU  A  66  .  ?        ?     ?  
67  1  1  A  67  ASN  A  67  .  ?        ?     ?  
#
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.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  OUTLIER       ?       ?  ?        15   9  0.78  12  0.85  molprobity  
 2   2  Cg_endo   -78.8   -79.4  OUTLIER   7   8  0.47  11  0.54  molprobity  
 3   3  p        -178.8   -43.1  OUTLIER   9   7  0.32  10  0.59  molprobity  
 4   4  t        -174.4    35.7  OUTLIER   5   6  0.21   8  0.43  molprobity  
 5   5  mt       -150.1    91.7  Allowed  11   8  0.28  11  0.89  molprobity  
 6   6  OUTLIER  -174.2   -72.9  OUTLIER   5   6  0.32   8  0.47  molprobity  
 7   7  p90       -75.1   -30.1  Favored   9  13  0.74  18  1.10  molprobity  
 8   8  mtp180    -59.3  -172.7  OUTLIER  13  11  0.74  14  0.82  molprobity  
 9   9  m         -56.4   135.1  Favored   4   6  0.30   9  0.92  molprobity  
10  10  Cg_endo   -82.5   -30.7  Allowed   7   8  0.45  11  0.56  molprobity  
11  11  m         -81.8   145.7  Favored   4   6  0.24   8  0.96  molprobity  
12  12  mtt180   -129.8   -46.4  Allowed  13  11  0.74  14  0.85  molprobity  
13  13  m-85     -118.3   134.2  Favored   9  12  0.86  16  0.79  molprobity  
14  14  m-85     -109.4   134.1  Favored   9  12  0.81  16  0.88  molprobity  
15  15  mm-40     -97.4    73.2  Favored   6   9  1.39  12  0.80  molprobity  
16  16  p         -60.4   -29.6  Favored   5   6  0.18   8  0.40  molprobity  
17  17  m170      -58.1   -21.3  Favored   7  11  0.47  15  0.71  molprobity  
18  18  t         -56.1   158.3  Allowed   9   7  0.30  10  0.82  molprobity  
19  19  ?        -146.3   140.2  Favored   5   5  0.22   7  0.47  molprobity  
20  20  ttt180    -43.0   -29.2  Allowed  13  11  0.77  14  0.83  molprobity  
21  21  ?         -60.4   -60.7  Favored   5   5  0.25   7  0.43  molprobity  
22  22  p-10      -78.3    -3.8  Favored   6   8  0.40  11  0.70  molprobity  
23  23  t         -80.1   134.1  Favored   9   7  0.37  10  0.65  molprobity  
24  24  tttt      -89.6   -53.1  Favored  13   9  0.37  11  0.78  molprobity  
25  25  t60      -148.0   167.8  Favored   7  11  0.46  15  0.73  molprobity  
26  26  mt       -122.8   144.8  Favored  11   8  0.39  11  0.90  molprobity  
27  27  mttt     -147.5   157.0  Favored  13   9  0.35  11  0.74  molprobity  
28  28  mt       -133.2   153.7  Favored  11   8  0.30  11  0.78  molprobity  
29  29  mt       -122.0   112.7  Favored  11   8  0.27  11  0.92  molprobity  
30  30  t-20      -81.8   105.8  Favored   6   8  0.41  11  0.77  molprobity  
31  31  OUTLIER  -118.6   144.1  Favored   7   7  0.26  11  0.86  molprobity  
32  32  Cg_endo   -82.9   -50.3  OUTLIER   7   8  0.48  11  0.58  molprobity  
33  33  m120      -59.7   -25.5  Favored   6   8  0.41  11  0.76  molprobity  
34  34  m        -123.1  -177.0  Favored   4   6  0.18   8  0.90  molprobity  
35  35  ?         -91.8  -166.5  Allowed   5   5  0.27   7  0.35  molprobity  
36  36  mt        -81.0    99.6  Favored  11   8  0.27  11  0.93  molprobity  
37  37  mp0       -85.6   104.7  Favored   8   9  0.44  12  0.75  molprobity  
38  38  mt        -74.2   119.4  Favored  11   8  0.39  11  0.88  molprobity  
39  39  m        -100.1   173.2  Allowed   9   7  0.32  10  0.67  molprobity  
40  40  ?        -161.2  -179.8  Favored   5   5  0.28   7  0.76  molprobity  
41  41  OUTLIER  -143.4   112.6  Favored  13  11  0.74  14  0.78  molprobity  
42  42  mt        -79.9   156.6  Favored  11   8  0.25  11  0.92  molprobity  
43  43  OUTLIER   -94.1   -59.6  Allowed  13   9  0.34  11  0.75  molprobity  
44  44  t-20      -48.9   -27.8  Favored   6   8  0.45  11  0.78  molprobity  
45  45  m-20     -104.3   -29.4  Favored   6   8  0.46  11  0.71  molprobity  
46  46  m-20       63.6    56.5  Allowed   6   8  0.43  11  0.79  molprobity  
47  47  mtp180   -156.7   168.8  Favored  13  11  0.73  14  0.82  molprobity  
48  48  tt0       -94.4   137.5  Favored   8   9  0.40  12  0.74  molprobity  
49  49  m        -147.1   157.6  Favored   9   7  0.31  10  0.78  molprobity  
50  50  m         -90.9   119.3  Favored   4   6  0.15   8  0.97  molprobity  
51  51  mt        -86.6   152.7  Favored  11   8  0.35  11  0.88  molprobity  
52  52  OUTLIER   -79.0   141.0  Favored   4   8  0.70  12  0.74  molprobity  
53  53  Cg_endo   -76.0   -18.9  Favored   7   8  0.51  11  0.58  molprobity  
54  54  mtpt      -93.5    13.7  Favored  13   9  0.35  11  0.76  molprobity  
55  55  mt        -65.4   159.2  Favored  11   8  0.35  11  0.85  molprobity  
56  56  mttt      -73.4   -39.1  Favored  13   9  0.40  11  0.77  molprobity  
57  57  p-90      -86.2   -27.4  Favored  10  16  0.67  23  1.43  molprobity  
58  58  mt        -81.1   -19.3  Favored  11   8  0.49  11  0.72  molprobity  
59  59  pt20      -68.4   -30.6  Favored   8   9  0.42  12  0.74  molprobity  
60  60  mt-10     -80.1   -35.4  Favored   6   9  1.40  12  0.84  molprobity  
61  61  t80       -68.9   -50.2  Favored   9  13  0.80  18  1.04  molprobity  
62  62  OUTLIER   -63.0   -28.1  Favored  11   8  0.27  11  0.88  molprobity  
63  63  tt0       -66.8   -48.0  Favored   6   9  1.41  12  0.79  molprobity  
64  64  OUTLIER   -85.2   -30.4  Favored  13   9  0.39  11  0.67  molprobity  
65  65  ?         -69.7   -38.0  Favored   5   5  0.26   7  0.45  molprobity  
66  66  tt        -75.4   -64.6  Allowed  11   8  0.28  11  0.91  molprobity  
67  67  m120          ?       ?  ?         6   8  0.47   8  0.93  molprobity  
#
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   1  N      1  0.41  2.83  
 2   2  CD     1  0.41  2.83  
 3   3  HG13   2  0.43  2.29  
 4   4  N      2  0.43  2.29  
 5   7  CE1    3  0.45  3.00  
 6   7  CD1    4  0.44  2.86  
 7   8  CG     3  0.45  3.00  
 8   8  N      4  0.44  2.86  
 9  10  CD     5  0.42  2.82  
10  15  O      6  0.49  2.08  
11  16  O      7  0.52  2.05  
12  18  CG1    8  0.55  2.32  
13  18  HG23   6  0.49  2.08  
14  18  HG12   9  0.40  2.30  
15  19  O     10  0.79  1.77  
16  19  N      9  0.40  2.30  
17  23  HG23  10  0.79  1.77  
18  23  HG22   8  0.55  2.32  
19  26  HD13  11  0.49  2.42  
20  26  HD21  12  0.47  1.85  
21  27  O     13  0.41  2.15  
22  28  HG21  14  0.42  1.91  
23  31  HG22  15  0.56  1.77  
24  32  HD2   15  0.56  1.77  
25  36  HD22  14  0.42  1.91  
26  37  NE2    5  0.42  2.82  
27  39  HG22  13  0.41  2.15  
28  51  CG2   16  0.69  2.16  
29  51  CG2   17  0.45  2.41  
30  51  HG22  18  0.54  1.78  
31  51  HG21  19  0.51  2.36  
32  51  HD12  12  0.47  1.85  
33  55  HD12  16  0.69  2.16  
34  55  HD12  18  0.54  1.78  
35  55  HD21   7  0.52  2.05  
36  58  CD1   19  0.51  2.36  
37  58  HD12  17  0.45  2.41  
38  61  CE2   11  0.49  2.42  
39  61  CE1   20  0.43  2.49  
40  65  HB2   20  0.43  2.49  
#
loop_
_pdbx_vrpt_instance_intra_plane_outliers.ordinal
_pdbx_vrpt_instance_intra_plane_outliers.instance_id
_pdbx_vrpt_instance_intra_plane_outliers.type
_pdbx_vrpt_instance_intra_plane_outliers.plane_rmsd
1   8  sidechain  0.30  
2  12  sidechain  0.28  
3  20  sidechain  0.19  
4  41  sidechain  0.20  
5  47  sidechain  0.30  
#
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  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  N  
##
