Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 14, 2015
Radiation
Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.0332 Å / Relative weight: 1
Reflection
Resolution: 2.8→60.427 Å / Num. obs: 38818 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 62.71 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Net I/σ(I): 9.85
Reflection shell
Resolution: 2.8→2.92 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.635 / Mean I/σ(I) obs: 2.1 / % possible all: 100
-
Processing
Software
Name
Version
Classification
PHENIX
1.10.1_2155
refinement
iMOSFLM
datareduction
SCALA
0.3.8
datascaling
PHASER
phasing
Refinement
Method to determine structure: SAD / Resolution: 2.8→60.427 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.65 Details: 5T3D is the replacement for 4ZXJ in which ligand was refined with incorrect stereochemistry. The only difference between 5T3D and 4ZXJ is that stereochemistry of the ligand was changed, ...Details: 5T3D is the replacement for 4ZXJ in which ligand was refined with incorrect stereochemistry. The only difference between 5T3D and 4ZXJ is that stereochemistry of the ligand was changed, followed by a single cycle of refinement.
Rfactor
Num. reflection
% reflection
Rfree
0.2319
1943
5.02 %
Rwork
0.1854
-
-
obs
0.1877
38741
99.94 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement step
Cycle: LAST / Resolution: 2.8→60.427 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7803
0
49
13
7865
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.012
8046
X-RAY DIFFRACTION
f_angle_d
1.307
11035
X-RAY DIFFRACTION
f_dihedral_angle_d
10.067
4807
X-RAY DIFFRACTION
f_chiral_restr
0.062
1277
X-RAY DIFFRACTION
f_plane_restr
0.008
1446
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.8002-2.8703
0.3499
149
0.3074
2551
X-RAY DIFFRACTION
100
2.8703-2.9479
0.2935
131
0.2721
2586
X-RAY DIFFRACTION
100
2.9479-3.0346
0.3366
136
0.2441
2580
X-RAY DIFFRACTION
100
3.0346-3.1326
0.3121
131
0.2443
2610
X-RAY DIFFRACTION
100
3.1326-3.2445
0.2753
141
0.2244
2585
X-RAY DIFFRACTION
100
3.2445-3.3744
0.2695
147
0.2131
2583
X-RAY DIFFRACTION
100
3.3744-3.528
0.2704
143
0.2167
2597
X-RAY DIFFRACTION
100
3.528-3.7139
0.2605
109
0.1836
2633
X-RAY DIFFRACTION
100
3.7139-3.9466
0.2222
132
0.1689
2609
X-RAY DIFFRACTION
100
3.9466-4.2512
0.1898
144
0.146
2633
X-RAY DIFFRACTION
100
4.2512-4.6789
0.1984
137
0.1484
2632
X-RAY DIFFRACTION
100
4.6789-5.3556
0.1922
150
0.1529
2658
X-RAY DIFFRACTION
100
5.3556-6.7461
0.2385
151
0.1917
2688
X-RAY DIFFRACTION
100
6.7461-60.4415
0.196
142
0.1711
2853
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
3.8567
-0.8017
-1.3108
4.5482
-0.1419
3.5451
0.5925
0.7834
0.6788
-0.8903
-0.2883
0.2757
-0.4327
-0.5687
-0.2709
0.8591
0.2971
0.1172
0.7672
0.075
0.5351
93.9377
99.2125
40.8226
2
3.3736
-2.625
-2.6761
3.9186
2.5559
6.3701
-0.069
-0.262
0.3652
0.246
0.2201
-0.1575
0.2463
0.2842
-0.1048
0.3995
0.0794
0.088
0.5177
0.0538
0.6928
88.8806
103.5162
66.6947
3
1.9135
-0.0458
-0.1728
1.5268
-0.117
3.0722
-0.0103
-0.1536
0.1768
0.1054
0.1387
0.0774
-0.6665
-0.3449
-0.1461
0.5428
0.0656
-0.0047
0.422
-0.0155
0.277
54.8539
135.8733
81.9713
4
5.6051
0.8311
-1.1367
4.6337
-0.7417
4.1977
0.0387
0.1563
-0.6751
-0.2362
0.0426
-0.106
0.3312
-0.3027
-0.0606
0.2988
-0.1018
-0.0354
0.3997
0.009
0.3545
49.4293
107.9354
72.8648
5
8.4011
-3.7664
4.4635
7.7407
-1.0776
3.0264
-0.0234
0.4373
-0.6625
-0.973
0.4342
1.2281
0.3448
-0.7312
-0.4484
0.5737
-0.1463
-0.1141
0.9378
0.2305
0.5305
36.0841
121.6814
58.0851
6
0.6642
-1.163
0.1585
4.7844
-0.1079
0.471
-0.2256
0.2039
0.3642
1.0664
-0.2429
-2.3178
-0.2964
0.5797
0.444
0.6257
-0.3419
-0.1087
0.9974
-0.2334
1.0845
87.3846
126.1376
80.9348
7
5.1293
-2.4658
3.9324
3.3545
-2.8373
3.5765
1.7241
-1.729
-3.1724
1.9804
-1.2982
-0.4698
0.8687
0.4832
-0.4614
1.3631
-0.7354
-0.5283
1.3613
0.2522
1.9198
32.0925
105.9074
56.6664
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' ((resseq4:186))
2
X-RAY DIFFRACTION
2
chain 'A' ((resseq187:429))
3
X-RAY DIFFRACTION
3
chain 'A' ((resseq445:857))
4
X-RAY DIFFRACTION
4
chain 'A' ((resseq858:964))
5
X-RAY DIFFRACTION
5
chain 'A' ((resseq972:1045))
6
X-RAY DIFFRACTION
6
chain 'A' ((resseq430:444))
7
X-RAY DIFFRACTION
7
chain 'A' ((resseq965:971))
+
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