Mass: 18.015 Da / Num. of mol.: 59 / 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
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Sample preparation
Crystal
Density Matthews: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal grow
Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris pH 8.0, 50 mM NaCl, 1.45-1.55 M (NH4)2SO4, 3% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
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Data collection
Diffraction
Mean temperature: 100 K
Diffraction source
Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
Resolution: 2.5→2.59 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.4 / % possible all: 99
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SOLVE
phasing
RESOLVE
phasing
PHENIX
1.5_2
refinement
PDB_EXTRACT
3.005
dataextraction
Blu-Ice
datacollection
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
version 1.5-2
phasing
Refinement
Method to determine structure: MAD; MOLECULAR REPLACEMENT Starting model: An initial model was generated using MAD data sets. This lower resolution model was used for molecular replacement with the final native data set. Resolution: 2.5→47.136 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 0.11 / Phase error: 25.11 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.2613
540
4.9 %
Rwork
0.2262
-
-
obs
0.2279
11031
95.17 %
all
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11594
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Solvent computation
Shrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.076 Å2 / ksol: 0.359 e/Å3
Displacement parameters
Biso mean: 62.965 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.315 Å2
0 Å2
0 Å2
2-
-
-2.315 Å2
-0 Å2
3-
-
-
4.629 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→47.136 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1868
0
37
59
1964
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.004
1924
X-RAY DIFFRACTION
f_angle_d
0.677
2591
X-RAY DIFFRACTION
f_dihedral_angle_d
16.175
757
X-RAY DIFFRACTION
f_chiral_restr
0.044
267
X-RAY DIFFRACTION
f_plane_restr
0.004
343
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.5001-2.7516
0.3028
129
0.27
2376
X-RAY DIFFRACTION
89
2.7516-3.1497
0.2784
125
0.2523
2577
X-RAY DIFFRACTION
95
3.1497-3.968
0.2434
144
0.188
2668
X-RAY DIFFRACTION
98
3.968-47.144
0.2464
142
0.2211
2870
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
0.0461
-0.1987
0.1924
0.6544
-0.7956
1.1456
-0.0637
-0.1104
0.0975
-0.0289
0.2456
-0.2053
-0.2164
-0.1096
-0.1251
0.184
-0.0411
0.0366
0.358
-0.0923
0.2261
-16.9604
40.1146
1.9113
2
1.2552
-0.2875
0.7592
1.869
0.4227
1.1294
-0.1172
-0.1238
0.3647
0.2224
0.5105
-0.3129
-0.0192
-0.0378
-0.2344
0.3513
-0.0116
0.086
0.4801
0.1208
0.312
-28.2435
35.2223
8.6079
3
1.6981
-0.574
0.51
1.5242
-0.1764
1.0002
0.2025
0.3801
-0.0409
-0.1855
-0.037
0.2025
-0.3766
-0.0673
-0.0281
0.4243
-0.1842
0.0759
0.3076
-0.0886
0.2885
-36.4358
28.7934
-10.0082
4
2.4293
-1.6895
-1.2411
3.3141
0.4323
2.2646
-0.3188
-0.3367
-0.0189
0.4503
0.7117
-0.1914
0.0082
-0.1341
-0.1452
0.4278
-0.1237
0.0108
0.2551
0.0157
0.3331
-43.5639
17.8464
-2.2036
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(chainAandresid9:70)
2
X-RAY DIFFRACTION
2
(chainBandresid9:63)
3
X-RAY DIFFRACTION
3
(chainCandresid8:65)
4
X-RAY DIFFRACTION
4
(chainDandresid8:64)
+
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