X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 35% PEG 8000, 0.2M sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 44.58 α = 90
b = 57.55 β = 90
c = 66.57 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++ -- 2012-03-05
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
2.04 50 99.5 0.073 -- -- 3.4 11338 11273 -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)
2.05 2.12 98.9 0.459 -- -- 3.2 1093

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 2.043 18.779 -- 0.0 11245 10956 1103 96.64 0.1962 0.1962 0.1923 0.23 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 2.0427 2.1356 -- 125 1093 0.257 0.321 -- 87.0
X Ray Diffraction 2.1356 2.248 -- 131 1176 0.2306 0.2983 -- 95.0
X Ray Diffraction 2.248 2.3886 -- 137 1220 0.2231 0.2756 -- 97.0
X Ray Diffraction 2.3886 2.5726 -- 137 1216 0.2161 0.2527 -- 97.0
X Ray Diffraction 2.5726 2.8307 -- 138 1234 0.1971 0.2139 -- 98.0
X Ray Diffraction 2.8307 3.2385 -- 141 1275 0.1877 0.2517 -- 99.0
X Ray Diffraction 3.2385 4.0733 -- 143 1286 0.1691 0.2054 -- 100.0
X Ray Diffraction 4.0733 18.7799 -- 151 1353 0.1784 0.1991 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.0413
Anisotropic B[1][1] 8.8786
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.7538
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.1248
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.849
f_plane_restr 0.006
f_chiral_restr 0.071
f_angle_d 1.046
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1169
Nucleic Acid Atoms 182
Heterogen Atoms 0
Solvent Atoms 125

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