data_5KTV

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  5KTV
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    5KTV
_pdbx_vrpt_summary.PDB_deposition_date         2016-07-12
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2024-01-10
_pdbx_vrpt_summary.report_creation_date        2024-01-04:01:44
_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      "DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*(1W5)P*GP*CP*G)-3')"  
2  non-polymer  "CALCIUM ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
E  2  
F  2  
G  2  
H  2  
I  2  
J  2  
K  2  
L  3  
M  3  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all   x-ray  
2  2.35  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore    
2  RSRZ_outliers_percent  
3  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   34.03  141614     ?     ?  
2  2  1   37.42    1232  2.36  2.36  
3  1  2  100.00  127900     ?     ?  
4  2  2  100.00    1150  2.36  2.36  
5  1  3   46.99  130704     ?     ?  
6  2  3   67.41    1164  2.36  2.36  
#
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  3  2  B  1  1  B  100.00  
4  4  2  B  1  1  B  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  1.07  0.58  232  354  
2  1  1  B  B  0.91  0.55  232  354  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       8.37
_pdbx_vrpt_summary_geometry.num_H_reduce     248
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   464
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.57
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  708
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.99
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 113.397
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            52.527
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         61.609
_pdbx_vrpt_summary_diffraction.I_over_sigma              2.04(2.34A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        2661
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.341
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.286
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.517
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.346
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.969
_pdbx_vrpt_summary_diffraction.twin_fraction             -1/3*h+1/3*k+1/3*l,-k,8/3*h+4/3*k+1/3*l:0.014;-2/3*h-1/3*k-1/3*l,-1/3*h-2/3*k+1/3*l,-4/3*h+4/3*k+1/3*l:0.022;-h,1/3*h-1/3*k-1/3*l,-4/3*h-8/3*k+1/3*l:0.009;-h,2/3*h+1/3*k+1/3*l,4/3*h+8/3*k-1/3*l:0.000;1/3*h+2/3*k-1/3*l,-k,-8/3*h-4/3*k-1/3*l:0.000;-1/3*h-2/3*k+1/3*l,-2/3*h-1/3*k-1/3*l,4/3*h-4/3*k-1/3*l:0.000;-h-k,k,-l:0.109
_pdbx_vrpt_summary_diffraction.DCC_R                     0.19
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.24
_pdbx_vrpt_summary_diffraction.EDS_R                     0.19
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.35
_pdbx_vrpt_summary_diffraction.EDS_res_low               33.48
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[69.245,69.245,44.180,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           0.412
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 17.58% 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         5
_pdbx_vrpt_summary_diffraction.centric_outliers          0
_pdbx_vrpt_summary_diffraction.data_completeness         99.74
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      109
_pdbx_vrpt_summary_diffraction.percent_free_reflections  4.10
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     0.00
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.35
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        34.05
_pdbx_vrpt_summary_diffraction.PDB_R                     0.18
_pdbx_vrpt_summary_diffraction.PDB_Rfree                 0.24
#
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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_mogul_angle_outliers
_pdbx_vrpt_model_instance.count_mogul_torsion_outliers
 1  1  1  A   2  DG   A    2  .  ?        ?     ?     ?     ?  
 2  1  1  A   3  DC   A    3  .  ?        ?     1     ?     ?  
 3  1  1  A   4  DG   A    4  .  ?        ?     1     ?     ?  
 4  1  1  A   5  DA   A    5  .  ?        ?     ?     ?     ?  
 5  1  1  A   6  DA   A    6  .  ?        ?     ?     ?     ?  
 6  1  1  A   7  DT   A    7  .  ?        ?     ?     ?     ?  
 7  1  1  A   8  DT   A    8  .  ?        1     ?     ?     ?  
 8  1  1  A   9  1W5  A    9  .  ?        ?     2     2     ?  
 9  1  1  A  10  DG   A   10  .  ?        ?     ?     ?     ?  
10  1  1  A  11  DC   A   11  .  ?        ?     ?     ?     ?  
11  1  1  A  12  DG   A   12  .  ?        ?     ?     ?     ?  
12  1  1  B   2  DG   B   14  .  ?        ?     ?     ?     ?  
13  1  1  B   3  DC   B   15  .  ?        ?     ?     ?     ?  
14  1  1  B   4  DG   B   16  .  ?        ?     ?     ?     ?  
15  1  1  B   5  DA   B   17  .  ?        ?     ?     ?     ?  
16  1  1  B   6  DA   B   18  .  ?        ?     ?     ?     ?  
17  1  1  B   7  DT   B   19  .  ?        ?     ?     ?     ?  
18  1  1  B   8  DT   B   20  .  ?        ?     1     ?     ?  
19  1  1  B   9  1W5  B   21  .  ?        ?     3     1     5  
20  1  1  B  10  DG   B   22  .  ?        ?     ?     ?     ?  
21  1  1  B  11  DC   B   23  .  ?        ?     2     ?     ?  
22  1  1  B  12  DG   B   24  .  ?        ?     ?     ?     ?  
23  1  2  C   .  CA   A  101  .  ?        ?     ?     ?     ?  
24  1  2  D   .  CA   A  102  .  ?        ?     ?     ?     ?  
25  1  2  E   .  CA   A  103  .  ?        ?     ?     ?     ?  
26  1  2  F   .  CA   A  104  .  ?        ?     ?     ?     ?  
27  1  2  G   .  CA   A  105  .  ?        ?     ?     ?     ?  
28  1  2  H   .  CA   B  101  .  ?        ?     ?     ?     ?  
29  1  2  I   .  CA   B  102  .  ?        ?     ?     ?     ?  
30  1  2  J   .  CA   B  103  .  ?        ?     ?     ?     ?  
31  1  2  K   .  CA   B  104  .  ?        ?     ?     ?     ?  
32  1  3  L   .  HOH  A  201  .  ?        ?     ?     ?     ?  
33  1  3  L   .  HOH  A  202  .  ?        ?     ?     ?     ?  
34  1  3  L   .  HOH  A  203  .  ?        ?     ?     ?     ?  
35  1  3  L   .  HOH  A  204  .  ?        ?     ?     ?     ?  
36  1  3  M   .  HOH  B  201  .  ?        ?     2     ?     ?  
37  1  3  M   .  HOH  B  202  .  ?        ?     ?     ?     ?  
38  1  3  M   .  HOH  B  203  .  ?        ?     ?     ?     ?  
39  1  3  M   .  HOH  B  204  .  ?        ?     ?     ?     ?  
40  1  3  M   .  HOH  B  205  .  ?        ?     ?     ?     ?  
41  1  3  M   .  HOH  B  206  .  ?        ?     ?     ?     ?  
42  1  3  M   .  HOH  B  207  .  ?        ?     ?     ?     ?  
43  1  3  M   .  HOH  B  208  .  ?        ?     ?     ?     ?  
44  1  3  M   .  HOH  B  209  .  ?        ?     ?     ?     ?  
45  1  3  M   .  HOH  B  210  .  ?        ?     ?     ?     ?  
46  1  3  M   .  HOH  B  211  .  ?        ?     ?     ?     ?  
47  1  3  M   .  HOH  B  212  .  ?        ?     ?     ?     ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_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    11   68.140    25  0.47    39  1.05  molprobity  1.000  
 2   2    11   76.950    21  0.60    32  1.22  molprobity  1.000  
 3   3    11   74.570    25  0.36    39  1.00  molprobity  1.000  
 4   4    11   82.410    24  0.82    37  1.15  molprobity  1.000  
 5   5    11   78.950    24  0.43    37  0.96  molprobity  1.000  
 6   6    12   74.660    22  0.52    34  1.03  molprobity  1.000  
 7   7    12   77.960    21  0.26    30  1.28  molprobity  1.000  
 8   8    11   76.830    18  0.66    20  1.11  mogul       1.000  
 9   9    11   61.100    25  0.56    39  1.11  molprobity  1.000  
10  10    11   54.090    21  0.92    32  0.66  molprobity  1.000  
11  11    12   62.420    24  0.58    35  1.10  molprobity  1.000  
12  12    11   72.150    25  0.62    39  1.01  molprobity  1.000  
13  13    11   61.850    21  0.61    32  1.06  molprobity  1.000  
14  14    11   61.080    25  0.28    39  0.82  molprobity  1.000  
15  15    11   64.910    24  0.48    37  0.83  molprobity  1.000  
16  16    11   65.710    24  0.39    37  0.84  molprobity  1.000  
17  17    12   69.990    22  0.51    34  1.01  molprobity  1.000  
18  18    12   73.550    21  0.50    30  1.04  molprobity  1.000  
19  19    11   88.720    18  0.68    20  1.08  mogul       1.000  
20  20    11   76.650    25  0.79    39  0.82  molprobity  1.000  
21  21    11   61.590    21  0.60    32  0.92  molprobity  1.000  
22  22    12   55.790    24  0.55    35  0.73  molprobity  1.000  
23  23     ?   95.130     ?     ?     ?     ?  ?           1.000  
24  24     ?  110.080     ?     ?     ?     ?  ?           1.000  
25  25     ?  104.900     ?     ?     ?     ?  ?           0.300  
26  26     ?   64.640     ?     ?     ?     ?  ?           1.000  
27  27     ?  104.720     ?     ?     ?     ?  ?           1.000  
28  28     ?  115.290     ?     ?     ?     ?  ?           0.330  
29  29     ?   72.510     ?     ?     ?     ?  ?           0.330  
30  30     ?  129.510     ?     ?     ?     ?  ?           0.330  
31  31     ?   66.120     ?     ?     ?     ?  ?           1.000  
32  32     ?   51.310     ?     ?     ?     ?  ?           1.000  
33  33     ?   55.670     ?     ?     ?     ?  ?           1.000  
34  34     ?   64.520     ?     ?     ?     ?  ?           1.000  
35  35     ?   85.810     ?     ?     ?     ?  ?           1.000  
36  36     ?   98.390     ?     ?     ?     ?  ?           1.000  
37  37     ?   21.820     ?     ?     ?     ?  ?           0.330  
38  38     ?   71.590     ?     ?     ?     ?  ?           1.000  
39  39     ?   65.150     ?     ?     ?     ?  ?           1.000  
40  40     ?   47.630     ?     ?     ?     ?  ?           1.000  
41  41     ?   60.830     ?     ?     ?     ?  ?           1.000  
42  42     ?   56.250     ?     ?     ?     ?  ?           1.000  
43  43     ?   52.980     ?     ?     ?     ?  ?           1.000  
44  44     ?   68.670     ?     ?     ?     ?  ?           1.000  
45  45     ?   72.610     ?     ?     ?     ?  ?           1.000  
46  46     ?   65.380     ?     ?     ?     ?  ?           1.000  
47  47     ?   55.490     ?     ?     ?     ?  ?           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   2  "H2''"  1  0.61  2.35  
 2   3  C8      1  0.61  2.35  
 3   8  P       2  1.48  1.10  
 4   8  OP2     2  1.48  1.10  
 5  18  "H2''"  3  0.52  1.91  
 6  19  P       4  1.47  1.07  
 7  19  OP1     4  1.47  1.07  
 8  19  "H5'A"  3  0.52  1.91  
 9  21  OP2     5  0.89  1.90  
10  21  P       6  0.82  2.36  
11  36  O       5  0.89  1.90  
12  36  O       6  0.82  2.36  
#
_pdbx_vrpt_instance_intra_angle_outliers.ordinal      1
_pdbx_vrpt_instance_intra_angle_outliers.instance_id  7
_pdbx_vrpt_instance_intra_angle_outliers.atom_1       "O5'"
_pdbx_vrpt_instance_intra_angle_outliers.atom_2       P
_pdbx_vrpt_instance_intra_angle_outliers.atom_3       OP1
_pdbx_vrpt_instance_intra_angle_outliers.obs          100.648
_pdbx_vrpt_instance_intra_angle_outliers.mean         105.700
_pdbx_vrpt_instance_intra_angle_outliers.stdev        0.900
_pdbx_vrpt_instance_intra_angle_outliers.Z            -5.61
#
loop_
_pdbx_vrpt_instance_mogul_angle_outliers.ordinal
_pdbx_vrpt_instance_mogul_angle_outliers.instance_id
_pdbx_vrpt_instance_mogul_angle_outliers.atom_1
_pdbx_vrpt_instance_mogul_angle_outliers.atom_2
_pdbx_vrpt_instance_mogul_angle_outliers.atom_3
_pdbx_vrpt_instance_mogul_angle_outliers.obsval
_pdbx_vrpt_instance_mogul_angle_outliers.mean
_pdbx_vrpt_instance_mogul_angle_outliers.numobs
_pdbx_vrpt_instance_mogul_angle_outliers.stdev
_pdbx_vrpt_instance_mogul_angle_outliers.Zscore
_pdbx_vrpt_instance_mogul_angle_outliers.mindiff
1   8  C5     C4     N4     121.80  125.22  33  1.03  -3.33  0.79  
2   8  "C4'"  "O4'"  "C1'"  104.65  108.83  52  2.07  -2.02  0.25  
3  19  C5     C4     N4     121.60  125.22  33  1.03  -3.52  0.99  
#
loop_
_pdbx_vrpt_instance_mogul_torsion_outliers.ordinal
_pdbx_vrpt_instance_mogul_torsion_outliers.instance_id
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_1
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_2
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_3
_pdbx_vrpt_instance_mogul_torsion_outliers.atom_4
_pdbx_vrpt_instance_mogul_torsion_outliers.obsval
_pdbx_vrpt_instance_mogul_torsion_outliers.mean
_pdbx_vrpt_instance_mogul_torsion_outliers.numobs
_pdbx_vrpt_instance_mogul_torsion_outliers.stdev
_pdbx_vrpt_instance_mogul_torsion_outliers.mindiff
_pdbx_vrpt_instance_mogul_torsion_outliers.local_density
1  19  C2     C1     "C1'"  "C2'"   140.98  53.43   40  15.18   5.73  2.50  
2  19  C2     C1     "C1'"  "O4'"  -100.88  53.82   43  14.79   6.80  2.33  
3  19  C6     C1     "C1'"  "C2'"   -35.95  54.21   43  14.61  12.80  0.00  
4  19  C6     C1     "C1'"  "O4'"    82.19  56.47   40  13.25  20.82  0.00  
5  19  "O4'"  "C4'"  "C5'"  "O5'"  -162.88  93.11  451  20.51   1.00  2.22  
#
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  22  0.964  0.092  -1.049  
 2   2  19  0.935  0.118  -0.570  
 3   3  22  0.952  0.134  -0.257  
 4   4  21  0.943  0.105  -0.760  
 5   5  21  0.939  0.094  -0.934  
 6   6  20  0.960  0.097  -0.928  
 7   7  20  0.968  0.099  -0.897  
 8   8  22  0.963  0.113       ?  
 9   9  22  0.966  0.111  -0.691  
10  10  19  0.989  0.114  -0.637  
11  11  22  0.974  0.130  -0.332  
12  12  22  0.944  0.112  -0.672  
13  13  19  0.966  0.129  -0.384  
14  14  22  0.974  0.114  -0.634  
15  15  21  0.968  0.104  -0.776  
16  16  21  0.960  0.099  -0.855  
17  17  20  0.933  0.137  -0.312  
18  18  20  0.951  0.114  -0.666  
19  19  22  0.929  0.156       ?  
20  20  22  0.957  0.122  -0.483  
21  21  19  0.984  0.121  -0.519  
22  22  22  0.967  0.113  -0.653  
23  23   1  0.887  0.102       ?  
24  24   1  0.955  0.371       ?  
25  25   1  0.965  0.477       ?  
26  26   1  0.996  0.050       ?  
27  27   1  0.913  0.156       ?  
28  28   1  0.943  0.387       ?  
29  29   1  0.940  0.054       ?  
30  30   1  0.353  0.072       ?  
31  31   1  0.980  0.096       ?  
32  32   1  0.982  0.196       ?  
33  33   1  0.980  0.647       ?  
34  34   1  0.818  0.151       ?  
35  35   1  0.712  0.554       ?  
36  36   1  0.991  0.173       ?  
37  37   1  0.862  0.347       ?  
38  38   1  0.962  0.527       ?  
39  39   1  0.929  0.458       ?  
40  40   1  0.950  0.100       ?  
41  41   1  0.964  0.237       ?  
42  42   1  0.784  0.259       ?  
43  43   1  0.930  0.142       ?  
44  44   1  0.887  0.215       ?  
45  45   1  0.877  0.136       ?  
46  46   1  0.881  0.229       ?  
47  47   1  0.959  0.304       ?  
#
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        "1.8.4, CSD as541be (2020)"                                           Y  
3  eds          2.36                                                                  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  
##
