X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.9
Temperature 295.0
Details PEG 8000, potassium chloride, glycerol, Tris, MES, UDP-GlcNAc, manganese chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.48 α = 90
b = 82.42 β = 90
c = 102.48 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-04-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F2 -- CHESS F2

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
1.5 38.24 94.2 0.065 -- -- 4.0 401605 99934 -- 0.0 12.9
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)
1.5 1.59 77.8 0.272 -- -- 4.5 31994

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
-- 1.5 38.24 0.0 0.0 -- 99934 4899 94.2 -- 0.166 0.166 0.194 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 1.5 1.59 -- 610 13087 0.207 0.253 0.01 77.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.4
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.58
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.6
c_dihedral_angle_d 24.9
c_bond_d 0.013
c_mcangle_it 2.1
c_improper_angle_d 1.1
c_scbond_it 2.55
c_mcbond_it 1.43
c_scangle_it 3.73
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.17
Luzzati Sigma A (R-Free Set) 0.12
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2780
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 516

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
CNS refinement version: 0.9