data_7ECH

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  7ECH
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   x-ray
#
_pdbx_vrpt_summary.entry_id                    7ECH
_pdbx_vrpt_summary.PDB_deposition_date         2021-03-12
_pdbx_vrpt_summary.PDB_revision_number         3
_pdbx_vrpt_summary.PDB_revision_date           2023-11-29
_pdbx_vrpt_summary.report_creation_date        2023-11-20:16:22
_pdbx_vrpt_summary.attempted_validation_steps  molprobity,validation-pack,xtriage,eds,mogul,buster-report,percentiles,writexml,writecif,writepdf
_pdbx_vrpt_summary.ligands_for_buster_report   Y
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*C)-3')"  
2  non-polymer  "POTASSIUM ION"  
3  water        water  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  1  
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  2.38  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  21.80  141614     ?     ?  
2  2  1  30.12    6082  2.36  2.40  
3  1  2   5.00  127900     ?     ?  
4  2  2   5.73    5397  2.36  2.40  
5  1  3  27.11  130704     ?     ?  
6  2  3  39.42    5509  2.36  2.40  
#
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    1.22  
4  4  2  B  1  1  B    1.32  
5  3  2  C  1  1  C    1.22  
6  4  2  C  1  1  C    1.32  
#
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  0.85  0.58  280  432  
2  1  1  B  B  0.80  0.59  300  460  
3  1  1  C  C  1.07  0.66  280  432  
#
_pdbx_vrpt_summary_geometry.ordinal          1
_pdbx_vrpt_summary_geometry.clashscore       11.78
_pdbx_vrpt_summary_geometry.num_H_reduce     414
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ   860
_pdbx_vrpt_summary_geometry.bonds_RMSZ       0.61
_pdbx_vrpt_summary_geometry.num_angles_RMSZ  1324
_pdbx_vrpt_summary_geometry.angles_RMSZ      0.91
#
_pdbx_vrpt_summary_diffraction.exp_method                x-ray
_pdbx_vrpt_summary_diffraction.ordinal                   1
_pdbx_vrpt_summary_diffraction.Babinet_b                 112.028
_pdbx_vrpt_summary_diffraction.bulk_solvent_b            40.781
_pdbx_vrpt_summary_diffraction.Wilson_B_estimate         54.168
_pdbx_vrpt_summary_diffraction.I_over_sigma              4.31(2.39A)
_pdbx_vrpt_summary_diffraction.num_miller_indices        3951
_pdbx_vrpt_summary_diffraction.Babinet_k                 0.335
_pdbx_vrpt_summary_diffraction.bulk_solvent_k            0.265
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L_mean     0.501
_pdbx_vrpt_summary_diffraction.Padilla_Yeates_L2_mean    0.340
_pdbx_vrpt_summary_diffraction.Fo_Fc_correlation         0.961
_pdbx_vrpt_summary_diffraction.DCC_R                     0.22
_pdbx_vrpt_summary_diffraction.DCC_Rfree                 0.26
_pdbx_vrpt_summary_diffraction.EDS_R                     0.21
_pdbx_vrpt_summary_diffraction.EDS_res_high              2.38
_pdbx_vrpt_summary_diffraction.EDS_res_low               39.05
_pdbx_vrpt_summary_diffraction.Wilson_B_aniso            "[97.489,36.634,46.391,0.000,0.000,0.000]"
_pdbx_vrpt_summary_diffraction.data_anisotropy           1.011
_pdbx_vrpt_summary_diffraction.trans_NCS_details         "The largest off-origin peak in the Patterson function is 9.66% 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         13
_pdbx_vrpt_summary_diffraction.centric_outliers          4
_pdbx_vrpt_summary_diffraction.data_completeness         97.77
_pdbx_vrpt_summary_diffraction.number_reflns_R_free      217
_pdbx_vrpt_summary_diffraction.percent_free_reflections  5.49
_pdbx_vrpt_summary_diffraction.percent_RSRZ_outliers     11.11
_pdbx_vrpt_summary_diffraction.PDB_resolution_high       2.38
_pdbx_vrpt_summary_diffraction.PDB_resolution_low        39.08
_pdbx_vrpt_summary_diffraction.PDB_R                     0.22
_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_angle_outliers
_pdbx_vrpt_model_instance.count_clashes
_pdbx_vrpt_model_instance.count_symm_clashes
_pdbx_vrpt_model_instance.ligand_of_interest
 1  1  1  A   1  DG   A    1  .  ?        ?     ?     ?  ?     
 2  1  1  A   2  DG   A    2  .  ?        ?     ?     ?  ?     
 3  1  1  A   3  DG   A    3  .  ?        ?     ?     ?  ?     
 4  1  1  A   4  DG   A    4  .  ?        ?     ?     ?  ?     
 5  1  1  A   5  DC   A    5  .  ?        ?     8     ?  ?     
 6  1  1  A   6  DC   A    6  .  ?        ?     1     ?  ?     
 7  1  1  A   7  DG   A    7  .  ?        ?     ?     ?  ?     
 8  1  1  A   8  DG   A    8  .  ?        1     1     ?  ?     
 9  1  1  A   9  DG   A    9  .  ?        ?     ?     ?  ?     
10  1  1  A  10  DG   A   10  .  ?        ?     ?     ?  ?     
11  1  1  A  11  DC   A   11  .  ?        ?     ?     1  ?     
12  1  1  A  12  DC   A   12  .  ?        ?     ?     ?  ?     
13  1  1  B   1  DG   B    1  .  ?        ?     ?     ?  ?     
14  1  1  B   2  DG   B    2  .  ?        ?     ?     ?  ?     
15  1  1  B   3  DG   B    3  .  ?        ?     ?     ?  ?     
16  1  1  B   4  DG   B    4  .  ?        ?     ?     ?  ?     
17  1  1  B   5  DC   B    5  .  ?        ?     4     ?  ?     
18  1  1  B   6  DC   B    6  .  ?        ?     ?     ?  ?     
19  1  1  B   7  DG   B    7  .  ?        ?     ?     ?  ?     
20  1  1  B   8  DG   B    8  .  ?        ?     ?     ?  ?     
21  1  1  B   9  DG   B    9  .  ?        ?     ?     ?  ?     
22  1  1  B  10  DG   B   10  .  ?        ?     ?     ?  ?     
23  1  1  B  11  DC   B   11  .  ?        ?     1     ?  ?     
24  1  1  B  12  DC   B   12  A  ?        ?     4     1  ?     
25  1  1  B  12  DC   B   12  B  ?        ?     1     ?  ?     
26  1  1  C   1  DG   C    1  .  ?        ?     ?     ?  ?     
27  1  1  C   2  DG   C    2  .  ?        ?     ?     ?  ?     
28  1  1  C   3  DG   C    3  .  ?        ?     ?     ?  ?     
29  1  1  C   4  DG   C    4  .  ?        ?     1     ?  ?     
30  1  1  C   5  DC   C    5  .  ?        ?     4     ?  ?     
31  1  1  C   6  DC   C    6  .  ?        ?     2     ?  ?     
32  1  1  C   7  DG   C    7  .  ?        ?     1     ?  ?     
33  1  1  C   8  DG   C    8  .  ?        3     ?     ?  ?     
34  1  1  C   9  DG   C    9  .  ?        ?     ?     ?  ?     
35  1  1  C  10  DG   C   10  .  ?        ?     ?     ?  ?     
36  1  1  C  11  DC   C   11  .  ?        ?     ?     ?  ?     
37  1  1  C  12  DC   C   12  .  ?        ?     ?     ?  ?     
38  1  2  D   .  K    A  101  .  ?        ?     ?     ?  Y     
39  1  2  E   .  K    A  102  .  ?        ?     ?     ?  Y     
40  1  2  F   .  K    A  103  .  ?        ?     ?     ?  Y     
41  1  2  G   .  K    A  104  .  ?        ?     ?     ?  Y     
42  1  2  H   .  K    B  101  .  ?        ?     ?     ?  Y     
43  1  2  I   .  K    B  102  .  ?        ?     ?     ?  Y     
44  1  2  J   .  K    C  101  .  ?        ?     ?     ?  Y     
45  1  2  K   .  K    C  102  .  ?        ?     ?     ?  Y     
46  1  3  L   .  HOH  A  201  .  ?        ?     ?     ?  ?     
47  1  3  L   .  HOH  A  202  .  ?        ?     ?     ?  ?     
48  1  3  L   .  HOH  A  203  .  ?        ?     ?     ?  ?     
49  1  3  L   .  HOH  A  204  .  ?        ?     ?     ?  ?     
50  1  3  M   .  HOH  C  201  .  ?        ?     ?     ?  ?     
51  1  3  M   .  HOH  C  202  .  ?        ?     ?     ?  ?     
#
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    12   49.490    22  0.68    35  0.59  molprobity  1.000  
 2   2    11   60.520    25  0.63    39  0.65  molprobity  1.000  
 3   3    11   58.850    25  0.58    39  0.76  molprobity  1.000  
 4   4    11   58.700    25  0.52    39  0.76  molprobity  1.000  
 5   5    11  127.780    21  0.58    32  1.10  molprobity  1.000  
 6   6    11  102.090    21  0.32    32  0.82  molprobity  1.000  
 7   7    11   58.190    25  0.59    39  0.79  molprobity  1.000  
 8   8    11   57.460    25  0.69    39  1.36  molprobity  1.000  
 9   9    11   57.810    25  0.62    39  0.85  molprobity  1.000  
10  10    11   53.210    25  0.57    39  0.89  molprobity  1.000  
11  11    11   60.380    21  0.65    32  0.69  molprobity  1.000  
12  12    12   77.130    20  0.46    28  0.44  molprobity  1.000  
13  13    12   48.470    22  0.91    35  0.57  molprobity  1.000  
14  14    11   53.930    25  0.63    39  0.63  molprobity  1.000  
15  15    11   60.170    25  0.45    39  0.71  molprobity  1.000  
16  16    11   68.780    25  0.48    39  0.64  molprobity  1.000  
17  17    11  146.650    21  0.53    32  1.03  molprobity  1.000  
18  18    11  116.080    21  0.26    32  0.68  molprobity  1.000  
19  19    11   58.420    25  0.52    39  0.62  molprobity  1.000  
20  20    11   61.440    25  0.79    39  1.22  molprobity  1.000  
21  21    11   70.480    25  0.46    39  0.74  molprobity  1.000  
22  22    11   68.850    25  0.59    39  0.67  molprobity  1.000  
23  23    11   91.980    21  0.62    32  1.08  molprobity  1.000  
24  24    12   86.650    20  0.59    28  0.74  molprobity  1.000  
25  25    12   86.650    20  0.59    28  0.74  molprobity  1.000  
26  26    12   57.510    22  0.61    35  0.66  molprobity  1.000  
27  27    11   66.720    25  0.68    39  0.87  molprobity  1.000  
28  28    11   65.300    25  0.62    39  0.66  molprobity  1.000  
29  29    11   71.770    25  0.43    39  0.99  molprobity  1.000  
30  30    11  147.590    21  0.62    32  1.82  molprobity  1.000  
31  31    11  156.380    21  0.60    32  1.16  molprobity  1.000  
32  32    11   70.180    25  0.78    39  1.12  molprobity  1.000  
33  33    11   62.710    25  0.87    39  1.56  molprobity  1.000  
34  34    11   59.940    25  0.74    39  0.78  molprobity  1.000  
35  35    11   53.080    25  0.72    39  0.99  molprobity  1.000  
36  36    11   62.250    21  0.58    32  0.86  molprobity  1.000  
37  37    12   80.520    20  0.38    28  0.63  molprobity  1.000  
38  38     ?   47.500     ?     ?     ?     ?  ?           0.500  
39  39     ?   46.310     ?     ?     ?     ?  ?           0.500  
40  40     ?   48.530     ?     ?     ?     ?  ?           0.500  
41  41     ?   44.400     ?     ?     ?     ?  ?           0.250  
42  42     ?   56.590     ?     ?     ?     ?  ?           1.000  
43  43     ?   51.550     ?     ?     ?     ?  ?           0.500  
44  44     ?   52.650     ?     ?     ?     ?  ?           1.000  
45  45     ?   46.170     ?     ?     ?     ?  ?           1.000  
46  46     ?   60.290     ?     ?     ?     ?  ?           1.000  
47  47     ?   45.460     ?     ?     ?     ?  ?           1.000  
48  48     ?   54.220     ?     ?     ?     ?  ?           1.000  
49  49     ?   64.940     ?     ?     ?     ?  ?           1.000  
50  50     ?   54.420     ?     ?     ?     ?  ?           1.000  
51  51     ?   57.940     ?     ?     ?     ?  ?           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   5  C6       1  1.27  1.69  
 2   5  C6       2  0.93  2.52  
 3   5  "H5''"   1  1.27  1.69  
 4   5  "H5''"   3  0.60  1.51  
 5   5  "C5'"    2  0.93  2.52  
 6   5  "C5'"    4  0.63  2.05  
 7   5  H6       4  0.63  2.05  
 8   5  H6       3  0.60  1.51  
 9   6  N3       5  0.68  2.08  
10   8  "H3'"    5  0.68  2.08  
11  17  C6       6  0.73  2.23  
12  17  "H5''"   6  0.73  2.23  
13  17  "H5''"   7  0.41  2.35  
14  17  N1       7  0.41  2.35  
15  23  "H2'"    8  0.43  2.18  
16  24  O2       9  0.53  2.54  
17  24  O2      10  0.50  2.12  
18  24  "C2'"    9  0.53  2.54  
19  24  "H2'"   10  0.50  2.12  
20  25  "O5'"    8  0.43  2.18  
21  29  "H4'"   11  0.42  2.02  
22  30  C6      12  0.47  2.50  
23  30  "H3'"   12  0.47  2.50  
24  30  C5      13  0.46  2.51  
25  30  "H5'"   11  0.42  2.02  
26  31  "H1'"   14  0.57  1.86  
27  31  "H5''"  13  0.46  2.51  
28  32  "H5''"  14  0.57  1.86  
#
loop_
_pdbx_vrpt_instance_symm_clashes.ordinal
_pdbx_vrpt_instance_symm_clashes.instance_id
_pdbx_vrpt_instance_symm_clashes.label_atom_id
_pdbx_vrpt_instance_symm_clashes.scid
_pdbx_vrpt_instance_symm_clashes.symop
_pdbx_vrpt_instance_symm_clashes.clashmag
_pdbx_vrpt_instance_symm_clashes.dist
1  11  N3  0  1_555  0.28  1.92  
2  24  N4  0  4_555  0.28  1.92  
#
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
_pdbx_vrpt_instance_intra_angle_outliers.link
1   8  "C4'"  "C3'"  "O3'"  122.690  112.300  2.000   5.20  ?     
2  33  P      "O3'"  "C3'"  125.707  119.700  1.200   5.01  Y     
3  33  "C1'"  "O4'"  "C4'"  104.949  110.100  1.000  -5.15  ?     
4  33  "C4'"  "C3'"  "O3'"  122.535  112.300  2.000   5.12  ?     
#
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  19  0.975  0.109  -0.728  
 2   2  22  0.947  0.125  -0.426  
 3   3  22  0.944  0.109  -0.728  
 4   4  22  0.965  0.119  -0.540  
 5   5  19  0.952  0.163   0.189  
 6   6  19  0.896  0.176   0.408  
 7   7  22  0.959  0.110  -0.709  
 8   8  22  0.945  0.129  -0.351  
 9   9  22  0.963  0.101  -0.879  
10  10  22  0.974  0.108  -0.747  
11  11  19  0.972  0.108  -0.739  
12  12  19  0.942  0.125  -0.452  
13  13  19  0.968  0.106  -0.785  
14  14  22  0.927  0.119  -0.540  
15  15  22  0.956  0.115  -0.615  
16  16  22  0.937  0.128  -0.370  
17  17  19  0.849  0.286   2.263  
18  18  19  0.902  0.185   0.560  
19  19  22  0.936  0.118  -0.558  
20  20  22  0.949  0.133  -0.275  
21  21  22  0.931  0.129  -0.351  
22  22  22  0.903  0.118  -0.558  
23  23  19  0.762  0.167   0.256  
24  24  38  0.679  0.370   3.680  
25  25  38  0.679  0.370   3.680  
26  26  19  0.969  0.120  -0.521  
27  27  22  0.944  0.102  -0.860  
28  28  22  0.937  0.099  -0.917  
29  29  22  0.922  0.139  -0.162  
30  30  19  0.759  0.287   2.280  
31  31  19  0.826  0.385   3.933  
32  32  22  0.959  0.173   0.479  
33  33  22  0.959  0.126  -0.408  
34  34  22  0.956  0.098  -0.936  
35  35  22  0.978  0.101  -0.879  
36  36  19  0.951  0.131  -0.351  
37  37  19  0.943  0.169   0.290  
38  38   1  0.979  0.112       ?  
39  39   1  0.974  0.156       ?  
40  40   1  0.968  0.129       ?  
41  41   1  0.987  0.034       ?  
42  42   1  0.967  0.117       ?  
43  43   1  0.960  0.155       ?  
44  44   1  0.974  0.121       ?  
45  45   1  0.934  0.149       ?  
46  46   1  0.720  0.267       ?  
47  47   1  0.846  0.323       ?  
48  48   1  0.774  0.318       ?  
49  49   1  0.916  0.094       ?  
50  50   1  0.825  0.248       ?  
51  51   1  0.828  0.399       ?  
#
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        unknown                                                               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  
##
