cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding Similarity search - Function
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9795 Å / Relative weight: 1
Reflection
Resolution: 2.8→100 Å / Num. obs: 59284 / % possible obs: 94.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 61 Å2 / Rsym value: 0.105 / Net I/σ(I): 12
Reflection shell
Resolution: 2.8→2.87 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2 / % possible all: 95.5
-
Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
XDS
datareduction
XSCALE
datascaling
PHASER
phasing
Coot
modelbuilding
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: two starting models were used for MR. One model contained residues 80-270 of CarH, determined by Co-SAD. Resolution: 2.8→70.65 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / Phase error: 27.91 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23
3027
5.11 %
Random selection
Rwork
0.183
-
-
-
obs
0.186
59232
94.8 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 75.9 Å2
Refinement step
Cycle: LAST / Resolution: 2.8→70.65 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
14668
0
872
0
15540
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.005
15981
X-RAY DIFFRACTION
f_angle_d
0.921
21964
X-RAY DIFFRACTION
f_dihedral_angle_d
11.252
6019
X-RAY DIFFRACTION
f_chiral_restr
0.036
2486
X-RAY DIFFRACTION
f_plane_restr
0.005
3141
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8001-2.8438
0.3555
151
0.3161
2582
X-RAY DIFFRACTION
95
2.8438-2.8904
0.3392
135
0.2896
2565
X-RAY DIFFRACTION
96
2.8904-2.9403
0.3009
148
0.2789
2585
X-RAY DIFFRACTION
95
2.9403-2.9937
0.3358
143
0.2723
2483
X-RAY DIFFRACTION
94
2.9937-3.0513
0.2954
126
0.2631
2575
X-RAY DIFFRACTION
93
3.0513-3.1136
0.3081
122
0.2522
2466
X-RAY DIFFRACTION
93
3.1136-3.1813
0.3308
146
0.257
2629
X-RAY DIFFRACTION
97
3.1813-3.2553
0.3174
138
0.2505
2568
X-RAY DIFFRACTION
96
3.2553-3.3367
0.3007
144
0.237
2570
X-RAY DIFFRACTION
96
3.3367-3.4269
0.2921
140
0.2134
2603
X-RAY DIFFRACTION
96
3.4269-3.5278
0.2633
125
0.1952
2537
X-RAY DIFFRACTION
95
3.5278-3.6416
0.2492
113
0.1828
2597
X-RAY DIFFRACTION
94
3.6416-3.7718
0.2193
150
0.1799
2473
X-RAY DIFFRACTION
92
3.7718-3.9228
0.2202
121
0.1727
2564
X-RAY DIFFRACTION
95
3.9228-4.1013
0.2074
132
0.1625
2579
X-RAY DIFFRACTION
96
4.1013-4.3175
0.1919
148
0.148
2581
X-RAY DIFFRACTION
96
4.3175-4.588
0.1859
151
0.1419
2552
X-RAY DIFFRACTION
95
4.588-4.9421
0.1928
139
0.1459
2503
X-RAY DIFFRACTION
93
4.9421-5.4393
0.22
144
0.1676
2553
X-RAY DIFFRACTION
95
5.4393-6.226
0.2269
126
0.1828
2605
X-RAY DIFFRACTION
96
6.226-7.8424
0.217
128
0.1638
2500
X-RAY DIFFRACTION
92
7.8424-70.6747
0.1597
157
0.1394
2535
X-RAY DIFFRACTION
95
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
2.6632
0.1276
-0.4571
1.7587
-0.5969
2.0198
0.0656
0.0829
-0.1453
-0.1624
-0.1739
-0.0409
0.0851
0.1438
0.1272
0.7709
0.1384
-0.0362
0.4847
0.0447
0.4437
-30.5387
5.0482
-7.2341
2
2.5125
-0.5573
0.3496
0.7441
-0.6677
1.8779
0.0542
-0.3075
0.1095
0.5967
0.0403
-0.0073
-0.3579
-0.1745
-0.1271
0.909
0.1338
-0.0113
0.5435
0.0114
0.4612
-35.5765
22.75
6.3236
3
2.5677
-1.14
-0.4676
2.2321
-0.9012
2.7892
0.0498
-0.1468
0.1234
0.2302
-0.1451
-0.089
-0.3836
0.2263
0.117
0.7953
0.0619
0.0151
0.5939
0.1061
0.5029
-23.3709
-5.6702
22.0414
4
4.9801
-0.572
1.5798
4.256
-1.6074
5.3429
0.1508
-0.2473
-0.102
0.3966
0.0032
0.303
0.0604
-0.2396
-0.1403
0.4321
0.0548
-0.0512
0.3903
-0.0516
0.3449
-31.2992
-12.8851
-30.1085
5
2.1881
0.4598
-1.7299
1.7892
-1.647
5.3095
0.0951
0.2094
-0.1322
-0.3505
0.0093
0.155
0.2506
-0.3331
-0.0882
0.7916
0.1138
-0.0193
0.5828
-0.0188
0.4648
-33.4546
-24.9064
15.8593
6
8.2547
0.9728
0.455
5.0629
1.6131
0.6243
0.545
0.3956
0.0492
-0.6717
0.1083
-0.0493
0.3469
-0.2335
-0.5258
0.4819
-0.0477
-0.1402
0.6028
0.105
0.4403
28.5344
-10.5437
-46.5834
7
4.1134
-0.2677
0.6603
2.0654
-1.0407
2.7733
0.0341
0.0054
0.0997
-0.0626
-0.0538
-0.1012
-0.1308
-0.1045
0.0164
0.5748
0.1009
0.0128
0.4399
0.0225
0.3614
-11.6587
-13.2043
-58.0001
8
3.1972
1.1412
1.4161
6.7156
-0.6458
5.0987
-0.0978
-0.1134
0.3411
0.0064
-0.17
-0.5292
-0.2899
0.3978
0.2995
0.7204
0.0307
0.0552
0.6708
0.1922
0.9852
-6.3414
-59.5173
-51.4913
9
2.6292
0.5805
-0.3927
1.8614
-1.8682
2.5128
0.1621
0.2187
-0.1853
-0.3664
-0.2737
-0.1527
0.7816
0.4446
0.1235
0.9528
0.2388
0.055
0.71
0.0524
0.5048
-2.1286
-29.6206
-71.1713
10
2.8882
2.312
-0.2001
1.9307
0.3055
3.175
0.2448
0.5783
-0.4602
-0.3328
0.0657
-0.3643
0.2732
0.7771
-0.3411
1.1209
0.5119
0.0036
1.099
0.1269
1.0268
24.7649
-41.1185
-56.9071
11
3.2903
-0.6347
-0.7696
2.1439
-1.0157
3.1794
-0.0409
-0.0268
-0.2439
-0.1264
0.0021
0.1293
0.383
0.1144
0.0376
0.5903
0.0756
-0.0483
0.4905
0.046
0.4251
-8.3193
-36.4974
-32.3247
12
0.7694
-0.2343
-2.155
4.6469
-1.3224
6.9348
0.023
-0.4244
0.2612
0.3976
0.7096
0.289
-1.0764
-0.5731
-0.8584
1.1856
0.093
-0.1496
1.057
0.1363
1.3509
2.8498
9.333
-45.583
13
3.4966
-1.5239
1.7057
2.2788
-1.3798
3.5495
0.0514
-0.1399
0.3633
0.321
-0.1886
-0.3162
-0.2538
0.1832
0.1347
0.4964
-0.0312
-0.0329
0.466
0.0882
0.5946
6.1044
-21.9508
-22.7307
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chain 'A' )
2
X-RAY DIFFRACTION
2
(chain 'B' )
3
X-RAY DIFFRACTION
3
(chain 'C' )
4
X-RAY DIFFRACTION
4
(chain 'D' andresid4through80)
5
X-RAY DIFFRACTION
5
(chain 'D' andresid81through301)
6
X-RAY DIFFRACTION
6
(chain 'E' andresid4through80)
7
X-RAY DIFFRACTION
7
(chain 'E' andresid81through301)
8
X-RAY DIFFRACTION
8
(chain 'F' andresid5through80)
9
X-RAY DIFFRACTION
9
(chain 'F' andresid81through301)
10
X-RAY DIFFRACTION
10
(chain 'G' andresid4through80)
11
X-RAY DIFFRACTION
11
(chain 'G' andresid81through301)
12
X-RAY DIFFRACTION
12
(chain 'H' and resid -6 through 80)
13
X-RAY DIFFRACTION
13
(chain 'H' andresid81through301)
+
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