- PDB-7pq3: Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islan... -
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Basic information
Entry
Database: PDB / ID: 7pq3
Title
Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in complex with its post-catalytic reaction product
Components
CRISPR-associated protein, APE2256 family
Keywords
ANTIVIRAL PROTEIN / RING NUCLEASE / CRISPR-ASSOCIATED PROTEIN / HELIX-TURN-HELIX / VIRAL RESISTANCE / CARF NUCLEOTIDE-BINDING DOMAIN / CRISPR Ring Nuclease
Function / homology
: / CRISPR system ring nuclease SSO1393 / CRISPR system ring nuclease SSO1393-like / CRISPR-associated protein (Cas_APE2256) / Chem-LQJ / CRISPR-associated protein, APE2256 family
Resolution: 2.85→48.05 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.91 / SU B: 61.199 / SU ML: 0.571 / Cross valid method: FREE R-VALUE / ESU R Free: 0.475 Details: Hydrogens have been added in their riding positions
Rfactor
Num. reflection
% reflection
Rfree
0.2906
740
5.01 %
Rwork
0.2515
14031
-
all
0.254
-
-
obs
-
14031
99.187 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 117.141 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.595 Å2
-0 Å2
-0 Å2
2-
-
-0.595 Å2
-0 Å2
3-
-
-
1.19 Å2
Refinement step
Cycle: LAST / Resolution: 2.85→48.05 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4358
0
88
0
4446
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.009
0.013
4538
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.017
4384
X-RAY DIFFRACTION
r_angle_refined_deg
1.638
1.644
6140
X-RAY DIFFRACTION
r_angle_other_deg
1.284
1.587
10144
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.863
5
535
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.572
23.909
220
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
21.725
15
859
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
18.63
15
18
X-RAY DIFFRACTION
r_chiral_restr
0.081
0.2
583
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
4929
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
967
X-RAY DIFFRACTION
r_nbd_refined
0.205
0.2
1005
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.214
0.2
4374
X-RAY DIFFRACTION
r_nbtor_refined
0.174
0.2
2131
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.083
0.2
2434
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.157
0.2
46
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.225
0.2
17
X-RAY DIFFRACTION
r_nbd_other
0.233
0.2
66
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.073
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
2.763
4.76
2146
X-RAY DIFFRACTION
r_mcbond_other
2.763
4.752
2144
X-RAY DIFFRACTION
r_mcangle_it
4.716
7.131
2679
X-RAY DIFFRACTION
r_mcangle_other
4.716
7.131
2679
X-RAY DIFFRACTION
r_scbond_it
3.098
5.213
2391
X-RAY DIFFRACTION
r_scbond_other
3.098
5.215
2392
X-RAY DIFFRACTION
r_scangle_it
5.195
7.711
3461
X-RAY DIFFRACTION
r_scangle_other
5.194
7.714
3462
X-RAY DIFFRACTION
r_lrange_it
11.251
90.028
17941
X-RAY DIFFRACTION
r_lrange_other
11.25
90.027
17942
X-RAY DIFFRACTION
r_ncsr_local_group_1
0.159
0.05
7708
Refine LS restraints NCS
Ens-ID
Dom-ID
Auth asym-ID
Refine-ID
Type
Rms dev position (Å)
Weight position
1
1
AAA
X-RAY DIFFRACTION
Localncs
0.15934
0.05008
1
2
BBB
X-RAY DIFFRACTION
Localncs
0.15934
0.05008
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Rfactor all
Num. reflection all
Fsc free
Fsc work
% reflection obs (%)
WRfactor Rwork
2.848-2.922
0.342
52
0.369
984
0.367
1044
0.65
0.687
99.2337
0.377
2.922-3.002
0.369
52
0.33
987
0.332
1039
0.773
0.778
100
0.335
3.002-3.088
0.416
51
0.34
968
0.343
1020
0.719
0.783
99.902
0.321
3.088-3.183
0.323
49
0.317
921
0.317
971
0.822
0.799
99.897
0.297
3.183-3.287
0.374
46
0.296
892
0.299
939
0.765
0.846
99.8935
0.275
3.287-3.402
0.341
46
0.278
884
0.281
930
0.843
0.866
100
0.256
3.402-3.529
0.336
46
0.275
866
0.279
921
0.872
0.861
99.0228
0.254
3.529-3.673
0.345
43
0.283
805
0.286
853
0.873
0.876
99.4138
0.259
3.673-3.835
0.24
42
0.249
793
0.249
838
0.903
0.913
99.642
0.234
3.835-4.021
0.274
40
0.25
763
0.251
809
0.908
0.912
99.2583
0.234
4.021-4.237
0.306
38
0.246
717
0.249
755
0.882
0.906
100
0.245
4.237-4.492
0.271
36
0.236
689
0.238
732
0.901
0.927
99.0437
0.239
4.492-4.799
0.255
35
0.236
650
0.238
687
0.925
0.928
99.7089
0.248
4.799-5.179
0.25
31
0.239
617
0.239
659
0.927
0.929
98.3308
0.259
5.179-5.667
0.247
31
0.247
574
0.247
606
0.936
0.923
99.835
0.272
5.667-6.324
0.433
26
0.289
524
0.295
552
0.763
0.898
99.6377
0.302
6.324-7.282
0.32
25
0.254
465
0.258
501
0.914
0.919
97.8044
0.284
7.282-8.868
0.273
21
0.204
393
0.208
429
0.943
0.955
96.5035
0.244
8.868-12.332
0.174
17
0.18
321
0.179
357
0.974
0.972
94.6779
0.236
12.332-48.048
0.332
13
0.26
218
0.264
246
0.862
0.946
93.9024
0.315
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.3983
-0.5446
1.0562
1.308
1.133
5.1215
-0.7458
-0.1786
-0.4295
0.3673
0.4841
0.1907
0.0076
0.3446
0.2617
0.9397
0.1219
0.1485
0.1773
0.0395
0.799
53.4713
17.5391
163.8041
2
2.3281
-1.0586
0.8717
1.9677
1.6767
3.527
-0.7058
0.0319
0.2479
-0.2086
0.4066
-0.1039
-1.2999
0.3562
0.2992
1.5238
-0.1355
-0.1256
0.2359
-0.0099
0.8547
49.9988
37.3263
151.5282
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
ALL
AAA
1 - 268
2
X-RAY DIFFRACTION
2
ALL
BBB
1 - 269
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