X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 25% PEG 8000, 0.2M ammonium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.85 α = 90
b = 56.78 β = 90
c = 66.26 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR RIGAKU RAXIS IV++ -- 2011-12-09
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R 1.54 -- --

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2 50 99.3 0.081 -- -- 3.4 12272 12182 -3.0 -3.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.0 2.07 93.4 0.463 -- -- 3.1 1123

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.1 31.408 -- 0.0 10557 10368 1043 98.19 0.1983 0.1983 0.1926 0.2479 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.1 2.2108 -- 140 1241 0.2163 0.2928 -- 94.0
X Ray Diffraction 2.2108 2.3492 -- 148 1296 0.2092 0.2872 -- 97.0
X Ray Diffraction 2.3492 2.5306 -- 142 1302 0.1976 0.2868 -- 98.0
X Ray Diffraction 2.5306 2.7851 -- 149 1324 0.1916 0.3056 -- 99.0
X Ray Diffraction 2.7851 3.1877 -- 151 1346 0.197 0.2492 -- 99.0
X Ray Diffraction 3.1877 4.0149 -- 153 1370 0.1724 0.2279 -- 100.0
X Ray Diffraction 4.0149 31.412 -- 160 1446 0.1972 0.2137 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 27.7296
Anisotropic B[1][1] 0.5949
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.4791
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.074
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.622
f_plane_restr 0.004
f_chiral_restr 0.084
f_angle_d 1.225
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 225
Heterogen Atoms 0
Solvent Atoms 138

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction