Resolution: 2.26→2.35 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4660 / % possible all: 97.7
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
SnB
phasing
RESOLVE
modelbuilding
PHENIX
(phenix.refine)
refinement
HKL-2000
datareduction
HKL-2000
datascaling
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.262→41.195 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 28.93 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2452
2372
5.1 %
RANDOM
Rwork
0.232
-
-
-
obs
0.2327
46479
99.34 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.734 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-12.0511 Å2
0 Å2
-0 Å2
2-
-
26.5038 Å2
-0 Å2
3-
-
-
-14.4527 Å2
Refinement step
Cycle: LAST / Resolution: 2.262→41.195 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3714
0
5
149
3868
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
3780
X-RAY DIFFRACTION
f_angle_d
1.441
5105
X-RAY DIFFRACTION
f_dihedral_angle_d
20.48
1349
X-RAY DIFFRACTION
f_chiral_restr
0.095
564
X-RAY DIFFRACTION
f_plane_restr
0.008
671
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.262-2.3081
0.3286
132
0.3248
2425
X-RAY DIFFRACTION
95
2.3081-2.3583
0.3408
153
0.3139
2567
X-RAY DIFFRACTION
98
2.3583-2.4132
0.3507
127
0.3089
2598
X-RAY DIFFRACTION
99
2.4132-2.4735
0.3191
120
0.2963
2581
X-RAY DIFFRACTION
99
2.4735-2.5404
0.2694
134
0.289
2625
X-RAY DIFFRACTION
99
2.5404-2.6151
0.3062
137
0.2652
2617
X-RAY DIFFRACTION
100
2.6151-2.6995
0.2791
144
0.2599
2606
X-RAY DIFFRACTION
100
2.6995-2.796
0.3249
137
0.248
2602
X-RAY DIFFRACTION
100
2.796-2.9079
0.2678
131
0.261
2640
X-RAY DIFFRACTION
100
2.9079-3.0402
0.3167
150
0.256
2625
X-RAY DIFFRACTION
100
3.0402-3.2004
0.3519
140
0.256
2565
X-RAY DIFFRACTION
100
3.2004-3.4009
0.2712
131
0.2313
2635
X-RAY DIFFRACTION
100
3.4009-3.6633
0.1991
140
0.2077
2602
X-RAY DIFFRACTION
100
3.6633-4.0317
0.1911
157
0.1798
2582
X-RAY DIFFRACTION
100
4.0317-4.6144
0.1653
152
0.1636
2626
X-RAY DIFFRACTION
100
4.6144-5.811
0.1891
158
0.179
2586
X-RAY DIFFRACTION
100
5.811-41.2017
0.2044
129
0.2342
2625
X-RAY DIFFRACTION
100
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
0.6735
0.2615
0.2365
1.2049
-0.8158
1.1712
-0.046
0.0092
0.0323
0.0623
0.014
-0.0687
0.1221
0.0066
-0
0.0658
0.0115
-0.0022
0.0626
-0.0468
0.0958
28.8424
28.8412
73.8941
2
0.626
-0.745
-0.1744
0.1384
-0.5987
1.3943
-0.0257
-0.09
0.0609
0.0218
0.016
-0.0726
-0.132
0.1009
0
0.1655
-0.0086
-0.0106
0.1818
-0.039
0.1871
25.6669
40.075
53.4853
3
0.366
-1.059
-0.1183
1.4983
-0.8937
1.022
-0.0663
0.1298
0.001
0.1028
-0.0231
-0.0052
0.0828
-0.4235
-0
0.137
-0.0288
0.004
0.2674
-0.0502
0.1486
20.6741
47.7308
110.3494
4
0.0686
-0.4812
-0.6726
1.6159
0.3423
1.1709
-0.0243
-0.0092
-0.0059
-0.072
0.0592
0.0276
-0.0151
0.4707
-0
0.1723
0.0474
-0.0035
0.2178
-0.0497
0.1354
37.5316
49.6016
93.1377
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
chainA
A
20 - 144
2
X-RAY DIFFRACTION
2
chainB
B
20 - 156
3
X-RAY DIFFRACTION
3
chainC
C
20 - 156
4
X-RAY DIFFRACTION
4
chainD
D
20 - 156
+
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