X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 293.0
Details 4.5% 2-propanol, 0.086M sodium citrate (pH5.5), 18% PEG 4000, 4.5% glycerol, 0.9% n-octyl-beta-D-glucopyranoside, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.05 α = 90
b = 77.33 β = 90
c = 136.39 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V -- 2006-07-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1

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
1.4 50 93.7 -- 0.039 -- 5.2 -- 147549 -- -- 12.1
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)
1.4 1.42 88.3 -- 0.197 4.1 3.1 6872

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 1.4 33.33 -- 0.0 -- 146494 7322 93.7 -- 0.165 0.165 0.185 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 1.4 1.42 -- 333 6457 0.293 0.279 0.015 88.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.1
Anisotropic B[1][1] 5.25
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.19
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.8
c_mcangle_it 1.73
c_improper_angle_d 1.09
c_scbond_it 2.9
c_angle_deg 1.6
c_dihedral_angle_d 22.7
c_bond_d 0.011
c_mcbond_it 1.22
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5299
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 940

Software

Software
Software Name Purpose
CNS refinement version: 1.2
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
SOLVE phasing