X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details PEG 8000, cacodylic acid, ammonium sulfate, DMSO, 2-mercaptoethanol with EP-UDPGlcNAc , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 178.99 α = 90
b = 178.99 β = 90
c = 178.99 γ = 90
Symmetry
Space Group I 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD SIEMENS -- 1998-06-12
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 17-ID 1.0332, 0.97939, 0.97928 APS 17-ID

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 10 94.4 0.075 -- -- 6.3 42374 39984 0.0 0.0 18.2
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 2.38 51.8 0.297 -- -- 6.0 --

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 2.3 10.0 2.0 2.0 42374 33156 3249 79.4 0.203 0.201 0.201 0.223 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 -- 405 3671 0.233 0.254 0.013 59.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.9
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 3.66
x_scbond_it 2.32
x_mcangle_it 1.84
x_mcbond_it 1.11
x_improper_angle_d 0.65
x_bond_d 0.008
x_angle_deg 1.4
x_dihedral_angle_d 25.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.23
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.24
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2345
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 213

Software

Computing
Computing Package Purpose
SAINT Data Reduction (intensity integration)
SAINT Data Reduction (data scaling)
MLPHARE Structure Solution
X-PLOR 98.0 Structure Refinement
Software
Software Name Purpose
X-PLOR(ONLINE) version: 98.0 refinement
MLPHARE model building