X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 294.0
Details 18% PEG 8000, 0.1M Na-cacodilate, 200mM Ca Ac2. Protein solution containing 5mM CaCl2 and 5 mM oligosaccharide (Dextra M592)., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.81 α = 90
b = 148.16 β = 91.03
c = 112.99 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-04-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL11-1 0.9646 SSRL BL11-1

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
2.5 50 97.8 0.053 -- -- -- 60699 59357 0.0 -3.0 43.0
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)
2.5 2.59 99.3 0.266 -- -- -- --

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
MOLECULAR REPLACEMENT 2.5 26.68 -- 0.0 60699 59357 3476 97.8 -- -- 0.213 0.258 shells
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 2.5 2.66 -- 654 8478 0.291 0.328 0.013 90.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.1
Anisotropic B[1][1] 5.49
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.72
Anisotropic B[2][2] 9.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -14.71
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.3
c_mcbond_it 1.35
c_scangle_it 3.08
c_improper_angle_d 0.78
c_bond_d 0.007
c_dihedral_angle_d 23.2
c_mcangle_it 2.26
c_scbond_it 2.08
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.42
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10443
Nucleic Acid Atoms 0
Heterogen Atoms 340
Solvent Atoms 252

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
COMO phasing
AMoRE phasing
CNS refinement version: 1.0