X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 295.0
Details PEG 400, zinc sulfate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.29 α = 90
b = 69.29 β = 90
c = 101.22 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-10-13
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 0.7 SPring-8 BL44B2

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
1.45 20 100.0 0.076 -- -- 11.2 31971 31954 -- 0.0 17.31
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)
1.45 1.5 100.0 0.286 -- -- -- --

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 1.45 10.0 -- 2.0 31866 31866 1602 99.4 -- -- 0.203 0.22 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 1.45 1.52 -- 165 3641 0.286 0.283 -- 95.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.89
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 24.073
x_mcbond_it 1.003
x_scbond_it 2.412
x_bond_d 0.005
x_mcangle_it 1.587
x_angle_deg 1.052
x_scangle_it 3.959
x_improper_angle_d 0.566
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.181
Luzzati Sigma A (Observed) 0.174
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.195
Luzzati Sigma A (R-Free Set) 0.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1297
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 231

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
DM model building
ARP/wARP model building
X-PLOR refinement version: 3.851
DM phasing