BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE BIOLOGICALLY RELEVANT OLIGIMERIZATION STATE.
Resolution: 2.1→29.93 Å / Num. obs: 100112 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 10.6
Reflection shell
Diffraction-ID: 1
Resolution (Å)
% possible obs (%)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
2.1-2.21
88.6
2.7
0.413
1.9
12939
0.413
2.21-2.35
99.5
3.4
0.271
2.8
13922
0.271
2.35-2.51
99.9
3.6
0.179
4.3
13156
0.179
2.51-2.71
100
3.6
0.121
6.3
12307
0.121
2.71-2.97
99.9
3.6
0.074
9.9
11310
0.074
2.97-3.32
99.8
3.6
0.05
13.4
10280
0.05
3.32-3.83
99.8
3.5
0.032
19.7
9081
0.032
3.83-4.7
99.6
3.5
0.032
17
7737
0.032
4.7-6.64
98.4
3.2
0.035
14.4
5954
0.035
6.64-29.93
98
3.4
0.022
22.5
3426
0.022
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→29.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.928 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. X-RAY FLUORESCENCE SUPPORTS THE ASSIGNMENT OF THE METAL SITES AS NICKEL. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. X-RAY FLUORESCENCE SUPPORTS THE ASSIGNMENT OF THE METAL SITES AS NICKEL. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.178
5004
5 %
RANDOM
Rwork
0.157
-
-
-
all
0.159
-
-
-
obs
0.15855
95035
97.81 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 44.232 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.67 Å2
0 Å2
0 Å2
2-
-
-1.91 Å2
0 Å2
3-
-
-
1.24 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→29.6 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6769
0
73
454
7296
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
7057
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
6472
X-RAY DIFFRACTION
r_angle_refined_deg
1.366
1.956
9583
X-RAY DIFFRACTION
r_angle_other_deg
0.812
3
15016
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.581
5
829
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.324
23.512
336
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.598
15
1211
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.305
15
39
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
1085
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
7646
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1477
X-RAY DIFFRACTION
r_nbd_refined
0.197
0.2
1348
X-RAY DIFFRACTION
r_nbd_other
0.182
0.2
6765
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
3386
X-RAY DIFFRACTION
r_nbtor_other
0.084
0.2
4237
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.136
0.2
451
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.18
0.2
6
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.318
0.2
31
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.114
0.2
6
X-RAY DIFFRACTION
r_mcbond_it
1.931
3
4916
X-RAY DIFFRACTION
r_mcbond_other
0.425
3
1694
X-RAY DIFFRACTION
r_mcangle_it
2.586
5
6797
X-RAY DIFFRACTION
r_scbond_it
4.691
8
3251
X-RAY DIFFRACTION
r_scangle_it
6.363
11
2786
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
1220
tightpositional
0.05
0.05
2
B
1220
tightpositional
0.04
0.05
3
C
1220
tightpositional
0.04
0.05
4
D
1220
tightpositional
0.04
0.05
1
A
1911
mediumpositional
0.42
0.5
2
B
1911
mediumpositional
0.32
0.5
3
C
1911
mediumpositional
0.35
0.5
4
D
1911
mediumpositional
0.32
0.5
1
A
1220
tightthermal
0.18
0.5
2
B
1220
tightthermal
0.14
0.5
3
C
1220
tightthermal
0.14
0.5
4
D
1220
tightthermal
0.16
0.5
1
A
1911
mediumthermal
0.94
2
2
B
1911
mediumthermal
0.76
2
3
C
1911
mediumthermal
0.74
2
4
D
1911
mediumthermal
0.77
2
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.275
283
-
Rwork
0.233
5940
-
obs
-
-
83.33 %
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
1.9226
-0.4606
-0.3304
2.3378
0.921
1.5398
-0.053
0.3108
-0.0005
-0.1965
0.0255
-0.0758
-0.1404
-0.0521
0.0275
-0.2604
-0.0168
-0.0302
-0.134
-0.0188
-0.2882
35.445
95.604
0.225
2
1.7064
0.4017
0.7574
3.0677
0.9881
1.5515
0.0073
-0.0821
0.043
0.1937
0.0594
-0.2988
-0.0226
0.0515
-0.0666
-0.1883
0.018
-0.1237
-0.2014
-0.0582
-0.1782
49.715
110.167
33.474
3
2.1477
-0.1582
0.7783
2.3211
0.937
2.057
-0.1016
-0.2242
0.3691
0.0586
-0.1247
0.2115
-0.2202
-0.2688
0.2263
-0.2189
0.076
-0.0721
-0.148
-0.081
-0.1476
18.662
114.572
24.048
4
1.2138
0.136
0.147
2.6908
-0.1956
1.5778
0.0298
-0.0573
-0.164
0.1885
0.0358
-0.0668
0.0304
-0.0668
-0.0656
-0.2112
0.0262
-0.0678
-0.2169
0.0329
-0.1997
34.723
79.217
28.492
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
-1 - 207
2
X-RAY DIFFRACTION
2
B
-1 - 207
3
X-RAY DIFFRACTION
3
C
-1 - 205
4
X-RAY DIFFRACTION
4
D
-1 - 206
+
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