X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details 1.39 M sodium citrate, 0.1 M HEPES, 0.2 M sodium thiocyanate, 10 mM dithiothreitol, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.92 α = 90
b = 46.92 β = 90
c = 168.8 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2010-05-28
Diffraction Radiation
Monochromator Protocol
Double silicon(111) crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.2822 NSLS X25

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
1.77 50 99.3 -- -- -- -- 19293 19167 2.0 1.0 --

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
SAD 1.77 45.207 -- 0.24 19293 19030 1903 98.35 -- 0.1906 0.1889 0.2057 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 1.7704 1.8337 -- 183 1648 0.1933 0.246 -- 97.0
X Ray Diffraction 1.8337 1.9071 -- 183 1646 0.1866 0.2404 -- 97.0
X Ray Diffraction 1.9071 1.9939 -- 183 1652 0.1909 0.2197 -- 98.0
X Ray Diffraction 1.9939 2.0991 -- 187 1675 0.1784 0.1955 -- 99.0
X Ray Diffraction 2.0991 2.2306 -- 191 1715 0.1765 0.1818 -- 99.0
X Ray Diffraction 2.2306 2.4028 -- 187 1689 0.1807 0.2368 -- 99.0
X Ray Diffraction 2.4028 2.6446 -- 192 1729 0.1945 0.2198 -- 99.0
X Ray Diffraction 2.6446 3.0272 -- 193 1740 0.2036 0.1913 -- 99.0
X Ray Diffraction 3.0272 3.8136 -- 196 1761 0.1889 0.197 -- 99.0
X Ray Diffraction 3.8136 45.2217 -- 208 1872 0.1813 0.1903 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -0.6285
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.6285
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.257
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.07
f_dihedral_angle_d 13.066
f_angle_d 1.038
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1231
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 152

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
SOLVE within PHENIX Structure Solution
PHENIX (phenix.refine: 1.6.1_357) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.6.1_357) refinement
SOLVE version: within PHENIX model building
CBASS data collection