X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 294.0
Details 8-13% polyethylene glycol, 100 mM Tris pH 8.0, 100 mM NaCl, 10 mM CaCl2, 100 mM a-Me-Man. The crystals were then transferred to a solution containing 200 mM methyl 3-O-(a-D-mannopyranosyl)-a-D-mannopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 130.06 α = 90
b = 38.69 β = 98.57
c = 55.03 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
IMAGE PLATE MARRESEARCH -- 1999-01-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1

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
2.3 100 99.3 0.064 -- -- 8.4 12333 12246 -- -3.0 22.8
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)
2.3 2.34 100.0 0.354 -- -- 2.9 603

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
-- 2.3 500.0 -- 0.0 -- 11589 1200 94.1 -- -- 0.212 0.262 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 2.3 2.44 -- 192 1612 0.26 0.304 0.022 89.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 37.2
Anisotropic B[1][1] 7.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.09
Anisotropic B[2][2] 1.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.42
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.75
c_scbond_it 1.55
c_angle_deg 1.4
c_mcangle_it 2.43
c_scangle_it 2.46
c_mcbond_it 1.36
c_dihedral_angle_d 23.1
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.37
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2204
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 115

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing