Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.94 Å3/Da / Density % sol: 58.12 %
Crystal grow
Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 2uL protein with 2uL well solution of 0.5 M ammonium sulfate, 0.9 M lithium sulfate,0.1M sodium citrate tribasic dihydrate , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 276K
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Data collection
Diffraction
Mean temperature: 93 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
Resolution: 2.15→2.23 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4920 / Rsym value: 0.584 / % possible all: 100
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Processing
Software
Name
Version
Classification
BOS
datacollection
PHASER
phasing
REFMAC
5.6.0117
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model Resolution: 2.15→47.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.892 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.22547
5003
10.1 %
RANDOM
Rwork
0.1859
-
-
-
all
0.18999
49462
-
-
obs
0.18999
44453
99.5 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 40.428 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.24 Å2
0 Å2
0 Å2
2-
-
-0.24 Å2
-0 Å2
3-
-
-
0.49 Å2
Refinement step
Cycle: LAST / Resolution: 2.15→47.4 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4990
0
30
192
5212
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.019
5150
X-RAY DIFFRACTION
r_angle_refined_deg
1.102
1.982
6972
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.378
5
645
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.774
23.442
215
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.995
15
899
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.666
15
37
X-RAY DIFFRACTION
r_chiral_restr
0.07
0.2
755
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
3857
LS refinement shell
Resolution: 2.151→2.195 Å / Total num. of bins used: 25
Rfactor
Num. reflection
% reflection
Rfree
0.285
280
-
Rwork
0.255
2470
-
obs
-
-
99.78 %
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
1.8312
-0.1817
0.1128
2.5824
0.4378
0.8857
0.0609
0.0242
0.2484
0.0209
-0.0711
-0.0842
0.0201
-0.0113
0.0102
0.0492
0.0468
0.0523
0.0517
0.0371
0.1295
45.6611
39.8679
-3.2365
2
1.1725
-0.1094
-0.4203
2.0695
-0.8527
1.4715
0.0207
0.098
-0.063
-0.0918
-0.0829
-0.0738
0.1698
0.0461
0.0622
0.1261
0.0466
0.0202
0.0335
0.003
0.0094
52.6668
12.6661
-4.293
3
2.0351
0.5796
0.0906
2.5433
0.2812
1.5748
-0.0073
-0.0448
0.0323
0.0192
-0.0085
-0.2448
-0.0211
0.0478
0.0158
0.016
0.0007
0.0098
0.0141
-0.0277
0.1124
30.8999
66.9831
2.5281
4
1.4675
0.0014
0.1007
2.0214
0.0261
2.4482
0.1088
-0.049
-0.0518
0.0152
-0.0585
0.0195
0.2715
0.0106
-0.0503
0.0459
-0.022
-0.0061
0.0792
0.0126
0.0127
17.4444
42.7844
1.0765
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
334 - 472
2
X-RAY DIFFRACTION
2
A
473 - 671
3
X-RAY DIFFRACTION
3
B
334 - 472
4
X-RAY DIFFRACTION
4
B
473 - 674
+
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