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_scangle_it 2.46
c_scbond_it 1.55
c_mcangle_it 2.43
c_mcbond_it 1.36
c_improper_angle_d 0.75
c_dihedral_angle_d 23.1
c_angle_deg 1.4
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 0.5 Structure Refinement
Software
Software Name Purpose
CNS version: 0.5 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection