Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.09 Å3/Da / Density % sol: 41.16 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; ...Details: Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
Monochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9 Å / Relative weight: 1
Reflection
Resolution: 1.3446→19.965 Å / Num. obs: 52020
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
1.7_650
refinement
PDB_EXTRACT
3.11
dataextraction
ADSC
Quantum
datacollection
HKL-2000
datareduction
PHENIX
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3446→18.835 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.12 / σ(F): 0 / Phase error: 14.86 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1704
1938
3.86 %
Rwork
0.1513
-
-
obs
0.1521
50200
92.98 %
all
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43062
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Solvent computation
Shrinkage radii: 0.05 Å / VDW probe radii: 0.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.024 Å2 / ksol: 0.534 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
-0.6172 Å2
0 Å2
0.5324 Å2
2-
-
-0.1419 Å2
0 Å2
3-
-
-
0.7591 Å2
Refinement step
Cycle: LAST / Resolution: 1.3446→18.835 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2044
0
43
261
2348
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.011
2257
X-RAY DIFFRACTION
f_angle_d
1.419
3083
X-RAY DIFFRACTION
f_dihedral_angle_d
12.745
849
X-RAY DIFFRACTION
f_chiral_restr
0.087
317
X-RAY DIFFRACTION
f_plane_restr
0.008
407
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.3446-1.3782
0.2454
113
0.2183
2873
X-RAY DIFFRACTION
78
1.3782-1.4155
0.2294
146
0.1955
3221
X-RAY DIFFRACTION
88
1.4155-1.4571
0.2036
128
0.1732
3304
X-RAY DIFFRACTION
90
1.4571-1.5041
0.1936
125
0.1622
3371
X-RAY DIFFRACTION
91
1.5041-1.5579
0.1801
136
0.1419
3400
X-RAY DIFFRACTION
92
1.5579-1.6202
0.1783
142
0.1387
3423
X-RAY DIFFRACTION
93
1.6202-1.6939
0.1537
142
0.1338
3522
X-RAY DIFFRACTION
95
1.6939-1.7831
0.1764
149
0.1365
3470
X-RAY DIFFRACTION
95
1.7831-1.8948
0.1426
132
0.1392
3574
X-RAY DIFFRACTION
96
1.8948-2.0409
0.1584
146
0.1366
3584
X-RAY DIFFRACTION
97
2.0409-2.246
0.1566
146
0.1405
3649
X-RAY DIFFRACTION
98
2.246-2.5703
0.161
149
0.141
3657
X-RAY DIFFRACTION
98
2.5703-3.2356
0.1711
148
0.1559
3722
X-RAY DIFFRACTION
99
3.2356-18.8367
0.1711
136
0.1653
3492
X-RAY DIFFRACTION
91
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
0.2376
-0.3421
-0.1338
0.5489
0.0919
0.4632
-0.034
0.0368
-0.1095
-0.0288
-0.0186
-0.1661
0.1561
0.327
0.0105
0.0863
0.0288
0.0144
0.1504
0.0076
0.135
8.6463
-4.5729
14.5804
2
0.5057
-0.1314
-0.1253
0.3762
0.0036
0.7167
-0.0557
-0.1744
0.0406
0.0756
0.0561
-0.0161
0.0813
0.149
0.0044
0.0882
0.0081
-0.0103
0.095
0.003
0.0791
-2.6661
-3.2007
28.6911
3
0.3507
-0.1681
0.2344
0.359
-0.0609
0.3859
-0.0024
-0.0238
0.1244
0.0218
0.0335
-0.0087
-0.0407
-0.1796
-0.0183
0.0966
0.0123
-0.0103
0.128
0.0135
0.098
-17.2541
5.5422
13.5733
4
0.2823
0.0392
-0.1498
0.2402
-0.0016
0.4509
-0.0131
0.0062
-0.0235
-0.0155
0.0153
0.0151
0.0326
-0.0302
0.0004
0.0837
-0.0022
-0.0034
0.0553
0.0046
0.0706
-11.6851
-3.4064
18.4337
5
0.6504
-0.0896
-0.0781
0.2114
-0.112
0.7133
0.0163
0.0644
-0.0002
-0.0241
-0.0061
-0.0077
0.0147
-0.0437
-0.0046
0.0697
-0.0049
-0.0039
0.0553
0.0011
0.0568
-11.6397
-1.7296
12.1541
6
0.3627
-0.0003
0.1233
0.262
-0.0427
0.3451
-0.0023
-0.0764
-0.0309
0.0325
0.0189
-0.0265
0.1422
0.0124
-0.0075
0.0921
-0.0025
-0.0043
0.0824
0.0074
0.0803
-5.3781
-6.0105
24.2784
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resseq4:19)
2
X-RAY DIFFRACTION
2
chain 'A' and (resseq20:39)
3
X-RAY DIFFRACTION
3
chain 'A' and (resseq40:77)
4
X-RAY DIFFRACTION
4
chain 'A' and (resseq78:115)
5
X-RAY DIFFRACTION
5
chain 'A' and (resseq116:238)
6
X-RAY DIFFRACTION
6
chain 'A' and (resseq239:261)
+
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