Group: Data collection / Category: diffrn / diffrn_source
Remark 700
SHEETS THE SHEET STRUCTURES OF CHAIN A, B, C, D, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS ... SHEETS THE SHEET STRUCTURES OF CHAIN A, B, C, D, E, F ARE BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED EACH FOR CHAINS A, B, C, D, E, F.
Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE FOUR N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG.
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Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3 Å3/Da / Density % sol: 59.1 % Description: SELENIUM SITES WERE IDENTIFIED IN DATA SET 2, COLLECTED AT 0.97950 A, PEAK DATA AT THE SE EDGE.
Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
1
1
2
0.9795
1
Reflection
Resolution: 2.4→49.1 Å / Num. obs: 28972 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 54 Å2 / Rsym value: 0.05 / Net I/σ(I): 18.1
Reflection shell
Resolution: 2.4→2.46 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.7 / % possible all: 99.8
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Processing
Software
Name
Classification
XDS
datareduction
XSCALE
datascaling
SHELX
phasing
PHASER
phasing
PHENIX
refinement
Refinement
Method to determine structure: SAD Starting model: NONE Resolution: 2.4→49.058 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 28.95 / Stereochemistry target values: ML Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUE 713. CHAIN B, RESIDUES 658, 730, 749. CHAIN C, RESIDUES ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. SIDE-CHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT CB ATOMS. CHAIN A, RESIDUE 713. CHAIN B, RESIDUES 658, 730, 749. CHAIN C, RESIDUES 656, 689, 729, 748. CHAIN D, RESIDUES 658, 749. CHAIN E, RESIDUES 658, 748. CHAIN F, RESIDUES 665, 693, 750.
Rfactor
Num. reflection
% reflection
Rfree
0.2566
1477
5.1 %
Rwork
0.2208
-
-
obs
0.2226
28937
99.42 %
Solvent computation
Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.347 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Biso mean: 69.1 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-20.1245 Å2
0 Å2
0 Å2
2-
-
-1.7364 Å2
0 Å2
3-
-
-
21.8609 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→49.058 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4984
0
0
76
5060
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
5153
X-RAY DIFFRACTION
f_angle_d
0.615
6932
X-RAY DIFFRACTION
f_dihedral_angle_d
15.912
1850
X-RAY DIFFRACTION
f_chiral_restr
0.044
653
X-RAY DIFFRACTION
f_plane_restr
0.002
862
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.4-2.4775
0.4555
131
0.3748
2438
X-RAY DIFFRACTION
99
2.4775-2.566
0.3655
157
0.3392
2448
X-RAY DIFFRACTION
100
2.566-2.6688
0.377
119
0.3234
2457
X-RAY DIFFRACTION
100
2.6688-2.7902
0.3791
128
0.3037
2497
X-RAY DIFFRACTION
100
2.7902-2.9373
0.3203
123
0.2664
2490
X-RAY DIFFRACTION
100
2.9373-3.1213
0.2465
120
0.2514
2470
X-RAY DIFFRACTION
100
3.1213-3.3622
0.2837
139
0.2331
2485
X-RAY DIFFRACTION
100
3.3622-3.7005
0.2518
144
0.2191
2486
X-RAY DIFFRACTION
99
3.7005-4.2357
0.2091
145
0.1944
2480
X-RAY DIFFRACTION
99
4.2357-5.3355
0.2042
139
0.1595
2522
X-RAY DIFFRACTION
99
5.3355-49.0679
0.2567
132
0.2123
2687
X-RAY DIFFRACTION
99
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
5.6676
0.6843
1.3889
4.599
-0.8389
6.1327
0.4224
0.7444
0.6701
-0.2695
0.0288
0.3815
-0.9838
-0.6548
0.0131
0.5702
0.1495
0.1773
0.5909
0.209
0.569
-34.1086
-39.8162
27.7998
2
6.5512
-0.6894
-1.5831
9.1102
-2.1732
5.342
0.3177
-0.505
1.2288
0.4031
0.169
-0.2896
-0.7961
0.2583
-0.3022
0.4361
-0.0502
0.1195
0.3168
-0.1563
0.4501
-16.3876
13.7832
4.4571
3
4.3544
1.83
2.6847
3.9555
1.4435
2.4157
0.7483
1.6702
-3.4395
-0.7797
0.7074
-0.0902
0.4233
1.1277
-0.498
0.5859
0.128
-0.3551
0.1398
-0.3106
1.4145
9.144
-21.4572
16.2225
4
7.3346
-2.0147
-3.7602
4.4791
0.8367
6.646
0.4123
-0.8048
0.9208
0.1296
0.51
-0.1595
-0.6088
0.3971
-0.8087
0.5433
0.0335
0.2013
0.3991
0.0247
0.5117
-16.9755
-39.8889
29.5638
5
2.3857
1.1614
1.989
7.3802
0.2896
5.98
0.1955
0.2707
0.8907
-0.1153
0.0043
0.8659
-0.6153
-0.1558
-0.0046
0.5439
0.0721
0.2257
0.4104
0.1159
0.7221
-33.3579
14.8015
2.4907
6
0.4717
-0.0648
-0.1394
-0.0423
0.0887
0.7355
0.1344
-0.5184
-1.2144
-0.153
0.5516
1.4491
0.7378
0.3685
0.0983
0.5209
-0.0297
-0.2274
0.2483
0.1092
1.2259
-7.8092
-22.1757
18.012
7
0.7157
-0.0935
-1.1659
0.9791
0.153
1.5178
0.2285
0.0057
-0.0694
0.1928
0.0198
0.3586
0.2087
-0.2119
0.0068
0.3702
0.0085
0.0998
0.5577
0.115
0.4274
-41.9775
-50.3244
40.2518
8
8.9548
-2.5602
-4.5894
5.5702
0.5404
8.0862
0.4898
1.0078
0.3559
-0.3276
-0.4371
-0.1958
-0.1
-0.2616
-0.0195
0.3713
-0.0211
-0.0239
0.5184
0.081
0.3278
-9.0513
10.498
-12.0015
9
3.7252
0.4717
4.0514
2.1945
0.622
6.5462
0.2438
-1.1672
-1.1016
0.3745
-0.0043
0.2364
-0.0132
-0.5085
-0.2567
0.3559
-0.0001
0.0188
0.5127
0.0658
0.5365
16.5155
-13.9528
31.435
10
6.0633
0.3456
-3.1858
5.4005
-0.7385
6.5369
0.2445
0.9445
0.5362
-0.3213
0.2411
-0.0292
0.1007
-0.0368
-0.4428
0.3728
0.012
-0.0179
0.4676
0.0498
0.2917
-9.6
-46.9347
14.4449
11
2.5556
0.0424
-1.6824
3.37
-0.521
3.5526
0.4363
-0.0146
0.3827
0.33
-0.1056
0.6013
0.1329
-0.3511
-0.3117
0.3424
0.0374
0.0684
0.3439
0.0563
0.4227
-41.8185
0.9842
11.2827
12
7.2134
-1.2772
3.7062
2.8641
-0.9825
4.5495
0.2399
0.5195
-1.2058
-0.0744
-0.0452
-0.0597
-0.0621
0.0243
-0.1932
0.2929
0.007
-0.013
0.2815
-0.0112
0.5008
-16.0403
-10.6605
6.5096
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND ((RESSEQ658:695))
2
X-RAY DIFFRACTION
2
CHAINBAND ((RESSEQ658:695))
3
X-RAY DIFFRACTION
3
CHAINCAND ((RESSEQ658:695))
4
X-RAY DIFFRACTION
4
CHAINDAND ((RESSEQ658:695))
5
X-RAY DIFFRACTION
5
CHAINEAND ((RESSEQ658:695))
6
X-RAY DIFFRACTION
6
CHAINFAND ((RESSEQ658:695))
7
X-RAY DIFFRACTION
7
CHAINAAND ((RESSEQ696:745))
8
X-RAY DIFFRACTION
8
CHAINBAND ((RESSEQ696:745))
9
X-RAY DIFFRACTION
9
CHAINCAND ((RESSEQ696:745))
10
X-RAY DIFFRACTION
10
CHAINDAND ((RESSEQ696:745))
11
X-RAY DIFFRACTION
11
CHAINEAND ((RESSEQ696:745))
12
X-RAY DIFFRACTION
12
CHAINFAND ((RESSEQ696:745))
+
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