X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.2
Temperature 298.0
Details PEG 300, Phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.76 α = 90
b = 75.76 β = 90
c = 41.8 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2006-03-10
CCD ADSC QUANTUM 4 Silicon II channel 2006-03-30
Diffraction Radiation
Monochromator Protocol
-- MAD
Silicon II channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 0.9789, 0.9793, 0.9640 SPring-8 BL26B1
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1

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
2.1 50 99.4 0.0062 -- -- 9.5 8314 8314 1.0 1.0 25.9
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)
2.1 2.18 95.7 0.329 -- -- 5.8 782

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 2.1 19.92 -- 0.0 8314 8265 678 99.5 -- 0.238 0.238 0.258 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 2.1 2.23 -- 103 1213 0.312 0.321 0.032 97.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.6
Anisotropic B[1][1] 9.39
Anisotropic B[1][2] 5.48
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 9.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -18.78
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 21.8
c_mcangle_it 2.38
c_angle_deg 1.1
c_bond_d 0.007
c_mcbond_it 1.52
c_scbond_it 2.99
c_scangle_it 4.34
c_improper_angle_d 0.73
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.29
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1023
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 78

Software

Software
Software Name Purpose
CNS refinement version: 1.1
ADSC data collection
CCP4 data scaling version: (SCALA)
SOLVE phasing