Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
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 coated 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: 1.45→19.965 Å / Num. obs: 40399
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
PHENIX
1.7.2_869
refinement
PDB_EXTRACT
3.11
dataextraction
ADSC
Quantum
datacollection
HKL-2000
datareduction
PHENIX
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.965 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 15.51 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Rfree
0.1844
2013
4.98 %
Rwork
0.1433
-
-
obs
0.1453
40397
93.81 %
all
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43062
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Solvent computation
Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.266 Å2 / ksol: 0.47 e/Å3
Displacement parameters
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0 Å2
Refinement step
Cycle: LAST / Resolution: 1.45→19.965 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2044
0
55
211
2310
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.009
2271
X-RAY DIFFRACTION
f_angle_d
1.27
3104
X-RAY DIFFRACTION
f_dihedral_angle_d
12.753
855
X-RAY DIFFRACTION
f_chiral_restr
0.081
319
X-RAY DIFFRACTION
f_plane_restr
0.007
410
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.45-1.4862
0.2313
139
0.1862
2739
X-RAY DIFFRACTION
94
1.4862-1.5264
0.216
143
0.167
2721
X-RAY DIFFRACTION
94
1.5264-1.5713
0.2299
141
0.1552
2730
X-RAY DIFFRACTION
94
1.5713-1.622
0.2116
138
0.1368
2685
X-RAY DIFFRACTION
93
1.622-1.6799
0.1912
141
0.1279
2676
X-RAY DIFFRACTION
92
1.6799-1.7472
0.2088
139
0.1086
2634
X-RAY DIFFRACTION
91
1.7472-1.8266
0.1354
139
0.111
2621
X-RAY DIFFRACTION
90
1.8266-1.9229
0.1612
135
0.1098
2647
X-RAY DIFFRACTION
90
1.9229-2.0432
0.1844
142
0.1195
2620
X-RAY DIFFRACTION
90
2.0432-2.2008
0.15
144
0.1249
2685
X-RAY DIFFRACTION
92
2.2008-2.4219
0.189
146
0.1278
2817
X-RAY DIFFRACTION
96
2.4219-2.7716
0.1678
153
0.1438
2903
X-RAY DIFFRACTION
99
2.7716-3.4889
0.1723
158
0.1594
2950
X-RAY DIFFRACTION
100
3.4889-19.9673
0.2099
155
0.1748
2956
X-RAY DIFFRACTION
98
+
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