X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.7
Temperature 293.0
Details 0.1M Magnesium acetate, 0.1M Sodium cacodylate pH6.7, 22.5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 180.97 α = 90
b = 180.97 β = 90
c = 100.75 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2005-12-09
CCD RIGAKU JUPITER 210 -- 2006-05-22
Diffraction Radiation
Monochromator Protocol
SI Double-Crystal SINGLE WAVELENGTH
SI Double-Crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.97904, 0.9000, 0.97942 SPring-8 BL26B2
SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.0000 SPring-8 BL26B2

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
1.65 50 100.0 0.04 -- -- 7.4 -- 148066 -- -- 18.8
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)
1.65 1.71 100.0 0.221 -- 6.2 6.7 --

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
MAD 1.65 47.96 -- 0.0 -- 148028 14786 99.8 -- 0.194 0.194 0.21 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 1.65 1.75 -- 2408 22267 0.215 0.24 0.005 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.4
Anisotropic B[1][1] 0.53
Anisotropic B[1][2] 1.11
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.06
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.71
c_improper_angle_d 0.8
c_mcbond_it 1.08
c_dihedral_angle_d 22.2
c_angle_deg 1.4
c_bond_d 0.005
c_scangle_it 2.66
c_scbond_it 1.83
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.06
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8318
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 622

Software

Software
Software Name Purpose
CNS refinement version: 1.1
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
SOLVE phasing