Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE FOUR N-TERMINAL RESIDUES REMAIN FROM THE EXPRESSION TAG.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 3.2 Å3/Da / Density % sol: 62 % Description: GOLD SITES WERE IDENTIFIED BY SIRAS, USING THE SECOND DATASET, COLLECTED AT 1.0397 A, PEAK DATA AT THE AU LIII-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
1.0397
1
Reflection
Resolution: 2.5→46 Å / Num. obs: 24355 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 51.51 Å2 / Rsym value: 0.07 / Net I/σ(I): 19.1
Reflection shell
Resolution: 2.5→2.56 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3 / Rsym value: 0.66 / % possible all: 100
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE)
refinement
XDS
datareduction
XSCALE
datascaling
SHELX
phasing
Refinement
Method to determine structure: SIRAS Starting model: NONE Resolution: 2.501→45.709 Å / SU ML: 0.3 / σ(F): 2.04 / Phase error: 21.04 / Stereochemistry target values: ML Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN B, RESIDUES 132 TO 134. CHAIN C, RESIDUES 132 TO 134, 151 TO 155, 180 TO 183 AND 302.
Rfactor
Num. reflection
% reflection
Rfree
0.2099
1244
5.1 %
Rwork
0.1672
-
-
obs
0.1694
24346
99.98 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 51.6 Å2
Refinement step
Cycle: LAST / Resolution: 2.501→45.709 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3951
0
0
74
4025
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
4031
X-RAY DIFFRACTION
f_angle_d
1.182
5460
X-RAY DIFFRACTION
f_dihedral_angle_d
14.14
1519
X-RAY DIFFRACTION
f_chiral_restr
0.06
623
X-RAY DIFFRACTION
f_plane_restr
0.006
699
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.5007-2.6008
0.2807
137
0.219
2533
X-RAY DIFFRACTION
100
2.6008-2.7191
0.2225
137
0.1967
2583
X-RAY DIFFRACTION
100
2.7191-2.8625
0.2324
155
0.1803
2536
X-RAY DIFFRACTION
100
2.8625-3.0418
0.2163
119
0.1869
2558
X-RAY DIFFRACTION
100
3.0418-3.2766
0.2412
129
0.1908
2578
X-RAY DIFFRACTION
100
3.2766-3.6062
0.2277
157
0.1777
2552
X-RAY DIFFRACTION
100
3.6062-4.1277
0.2325
132
0.1588
2574
X-RAY DIFFRACTION
100
4.1277-5.1993
0.1686
141
0.1441
2570
X-RAY DIFFRACTION
100
5.1993-45.717
0.192
137
0.157
2618
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
2.8746
0.3272
-0.7561
1.5303
0.2228
0.9753
-0.1378
-0.3414
0.4466
0.2146
0.0956
0.2639
-0.2912
-0.3924
-0.0001
0.3934
0.059
-0.0032
0.3982
-0.0359
0.361
18.4884
72.1829
-7.961
2
3.9279
0.3218
-0.6802
3.7739
1.2377
2.1259
-0.2513
-0.1746
-0.3952
0.3022
0.0845
0.1596
0.14
0.0519
-0.0061
0.3692
0.0257
0.0598
0.2601
0.0597
0.3388
45.2545
44.3219
9.4634
3
3.9202
0.2448
0.4609
2.8752
2.5218
2.3146
-0.1593
-0.3464
-0.703
0.3748
0.0551
0.6364
0.6415
-0.6022
-0.0079
0.4295
-0.0279
0.1227
0.4207
0.0433
0.6522
34.8001
38.0323
9.9574
4
3.446
0.7309
1.7284
1.0545
-0.5704
2.9909
-0.2276
0.0171
0.4924
-0.0593
0.087
0.0976
-0.4785
0.0008
-0.0071
0.3658
0.0391
-0.0889
0.2897
-0.032
0.3061
31.6908
77.3539
-12.7442
5
1.6841
-0.6504
0.9965
1.288
0.5964
1.5468
0.0218
0.9174
0.5047
-0.7263
-0.1309
0.2876
0.0961
0.1345
-0.0047
0.6967
0.0508
0.0303
0.9445
0.2371
0.4902
57.3093
74.8599
-32.7893
6
2.4839
-0.3256
0.0263
2.2522
0.3522
2.8234
0.0626
0.488
-0.5976
-0.5274
-0.1222
0.6241
-0.1767
-0.3872
-0.0139
0.43
-0.0035
-0.0696
0.5898
-0.1886
0.5501
50.4201
36.8792
-21.6479
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
CHAINAAND (RESID132THROUGH200 )
2
X-RAY DIFFRACTION
2
CHAINAAND (RESID201THROUGH302 )
3
X-RAY DIFFRACTION
3
CHAINBAND (RESID135THROUGH200 )
4
X-RAY DIFFRACTION
4
CHAINBAND (RESID238THROUGH302 )
5
X-RAY DIFFRACTION
5
CHAINCAND (RESID135THROUGH200 )
6
X-RAY DIFFRACTION
6
CHAINCAND (RESID201THROUGH301 )
+
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