X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 4.8
Temperature 293.0
Details PEG 3350, sodium acetate, pH 4.8, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 100.35 α = 90
b = 100.35 β = 90
c = 45.77 γ = 90
Symmetry
Space Group I 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU JUPITER 210 -- 2004-10-10
CCD ADSC QUANTUM 4 -- 2004-10-03
Diffraction Radiation
Monochromator Protocol
Si double crystals SINGLE WAVELENGTH
SI(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 0.97885, 0.97920, 0.97300 Photon Factory BL-6A
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
1.9 50 99.8 -- 0.061 -- 7.3521 -- 18141 -- -- --
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)
1.9 1.97 100.0 -- 0.398 2.9713 7.5 1790

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 2.0 35.5 -- 0.0 -- 15498 1200 99.5 -- -- 0.1844 0.2112 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 2.0 2.09 1754 145 2347 0.253 0.288 0.023 99.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 43.5
Anisotropic B[1][1] -1.27
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.53
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_scbond_it 2.23
c_scangle_it 3.57
c_angle_deg 1.2
c_dihedral_angle_d 22.1
c_mcangle_it 2.43
c_improper_angle_d 0.61
c_mcbond_it 1.38
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1080
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 54

Software

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