transcription regulator / alpha-beta-alpha sandwich / helix-turn-helix / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information
response to arsenic-containing substance / negative regulation of DNA-templated transcription / DNA binding / metal ion binding Similarity search - Function
Resolution: 2.1→2.14 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.47 / Num. unique all: 1616 / Rsym value: 0.743 / % possible all: 100
-
Processing
Software
Name
Version
Classification
SBC-Collect
datacollection
HKL-3000
datacollection
HKL-3000
phasing
SHELXS
phasing
MLPHARE
phasing
RESOLVE
modelbuilding
SOLVE
phasing
PHENIX
(phenix.refine: 1.5_2)
refinement
HKL-3000
datareduction
HKL-3000
datascaling
RESOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.1→27.32 Å / SU ML: 0.34 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL / Details: both F+ and F- are used for refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.219
3016
5.05 %
random
Rwork
0.172
-
-
-
all
0.175
59741
-
-
obs
0.175
32257
94.11 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.017 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
1.4642 Å2
0 Å2
0 Å2
2-
-
1.4642 Å2
0 Å2
3-
-
-
-2.9284 Å2
Refinement step
Cycle: LAST / Resolution: 2.1→27.32 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3213
0
27
487
3727
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.013
3355
X-RAY DIFFRACTION
f_angle_d
1.396
4548
X-RAY DIFFRACTION
f_dihedral_angle_d
19.114
1262
X-RAY DIFFRACTION
f_chiral_restr
0.091
538
X-RAY DIFFRACTION
f_plane_restr
0.006
588
LS refinement shell
Refine-ID: X-RAY DIFFRACTION
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection obs
% reflection obs (%)
2.1-2.175
0.3325
265
0.2791
4939
5204
83
2.175-2.2621
0.2841
307
0.2419
5268
5575
87
2.2621-2.365
0.2684
303
0.2063
5452
5755
90
2.365-2.4896
0.2399
303
0.1849
5586
5889
93
2.4896-2.6455
0.226
248
0.1867
5791
6039
95
2.6455-2.8495
0.2243
303
0.1878
5763
6066
96
2.8495-3.1359
0.2338
319
0.188
5927
6246
98
3.1359-3.5888
0.2174
321
0.1729
5975
6296
100
3.5888-4.5182
0.1806
357
0.1354
5984
6251
100
4.5182-27.3228
0.1683
290
0.1329
6040
6330
99
Refinement TLS params.
Refine-ID: X-RAY DIFFRACTION
ID
Method
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
refined
4.1049
2.3413
1.6697
2.3098
1.3042
2.5263
0.8053
-0.7374
-0.6106
1.046
-0.4615
-0.6812
0.1834
-0.2043
-0.2722
0.5007
-0.1442
-0.2366
0.3115
0.1801
0.3638
33.1719
59.8593
14.812
2
3.4009
0.1046
-1.6692
2.6949
-0.4216
2.3251
-0.0266
-0.1905
0.2103
0.3466
0.0192
0.0877
-0.1557
0.0083
0.0209
0.2122
0.0678
0.0164
0.3615
-0.0676
0.1926
3
2.9015
-0.3489
1.8141
2.3025
0.5118
4.638
0.2129
0.4066
0.0414
0.0919
-0.0452
0.0354
0.4175
-0.2992
-0.1216
0.2204
-0.0694
0.0016
0.3937
0.0402
0.1924
4
3.325
0.5429
0.9046
3.1837
0.108
1.8047
0.0588
0.0787
0.0901
-0.0299
0.0015
0.1886
0.0115
-0.0355
-0.0492
0.1596
-0.0082
-0.0271
0.2264
0.0535
0.2447
Refinement TLS group
Selection details: chain D
+
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