Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97924 Å / Relative weight: 1
Reflection
Resolution: 2.498→44.7 Å / Num. all: 14207 / Num. obs: 14207 / % possible obs: 99.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 36.36 Å2 / Rsym value: 0.122 / Net I/σ(I): 11.26
Reflection shell
Resolution: 2.498→2.54 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 1.82 / % possible all: 100
-
Processing
Software
Name
Version
Classification
HKL-3000
datacollection
HKL-3000
datascaling
HKL-3000
phasing
PHENIX
1.9_1692
refinement
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: The 2.4 A structure of Apo-protein solved by SAD phasing Resolution: 2.498→44.696 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.269
758
3 %
Random selection
Rwork
0.2303
-
-
-
obs
0.2314
13940
98.52 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Biso mean: 36.9 Å2
Refinement step
Cycle: LAST / Resolution: 2.498→44.696 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2609
0
64
52
2725
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.003
2715
X-RAY DIFFRACTION
f_angle_d
0.618
3665
X-RAY DIFFRACTION
f_dihedral_angle_d
13.384
989
X-RAY DIFFRACTION
f_chiral_restr
0.024
397
X-RAY DIFFRACTION
f_plane_restr
0.002
461
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.4985-2.6914
0.3535
146
0.3032
4733
X-RAY DIFFRACTION
95
2.6914-2.9622
0.2915
160
0.2806
4936
X-RAY DIFFRACTION
100
2.9622-3.3907
0.3168
149
0.243
4950
X-RAY DIFFRACTION
100
3.3907-4.2714
0.2402
157
0.2076
4947
X-RAY DIFFRACTION
100
4.2714-44.7031
0.2389
146
0.2038
4902
X-RAY DIFFRACTION
99
+
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