X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 30% PEG 6000, 0.2M lithium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.76 α = 90
b = 58.18 β = 90
c = 65.63 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++ -- 2012-03-08
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
1.78 50 99.5 0.036 -- -- 3.5 15437 15354 -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)
1.79 1.85 99.5 0.192 -- -- 3.4 1492

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 1.783 17.512 -- 0.0 15326 15243 1527 98.75 0.1769 0.1769 0.1737 0.2069 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 1.7828 1.8402 -- 129 1130 0.2314 0.2705 -- 92.0
X Ray Diffraction 1.8402 1.9059 -- 135 1218 0.1934 0.2346 -- 98.0
X Ray Diffraction 1.9059 1.9821 -- 135 1224 0.1758 0.2662 -- 99.0
X Ray Diffraction 1.9821 2.0722 -- 137 1237 0.1698 0.2406 -- 100.0
X Ray Diffraction 2.0722 2.1813 -- 138 1249 0.1669 0.1938 -- 100.0
X Ray Diffraction 2.1813 2.3177 -- 139 1242 0.1716 0.2011 -- 100.0
X Ray Diffraction 2.3177 2.4961 -- 139 1251 0.1768 0.2239 -- 100.0
X Ray Diffraction 2.4961 2.7465 -- 142 1274 0.1824 0.2106 -- 100.0
X Ray Diffraction 2.7465 3.1419 -- 141 1263 0.1704 0.1964 -- 100.0
X Ray Diffraction 3.1419 3.951 -- 141 1281 0.1564 0.2035 -- 100.0
X Ray Diffraction 3.951 17.5129 -- 151 1347 0.1788 0.182 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.3169
Anisotropic B[1][1] -0.7795
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.029
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.2495
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.98
f_plane_restr 0.005
f_chiral_restr 0.077
f_angle_d 1.144
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1169
Nucleic Acid Atoms 188
Heterogen Atoms 0
Solvent Atoms 184

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