X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 293.0
Details 1.3 to 1.6 M Sodium Acetate, 10 mM MnCl2, 10 mM Hg-UDP-galactgose, 500 mM NaCl, 100 mM cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.61 α = 90
b = 95.61 β = 90
c = 110.72 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2000-10-10
Diffraction Radiation
Monochromator Protocol
graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.9324 ESRF ID14-3

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 15 98.7 0.043 -- -- 6.7 452447 18010 1.0 1.0 56.2
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)
2.5 2.66 99.4 0.227 -- 2.4 6.4 --

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 15.0 0.0 0.0 452447 18010 1804 98.7 0.224 0.224 0.224 0.272 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 2.5 2.66 2682 306 -- 0.341 0.41 0.023 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -15.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -15.4
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 30.81
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.015
c_angle_d 1.8
c_dihedral_angle_d 24.7
c_improper_angle_d 2.27
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.36
Luzzati Sigma A (Observed) 0.45
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 0.57
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2306
Nucleic Acid Atoms 0
Heterogen Atoms 49
Solvent Atoms 97

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.0
DENZO data reduction
CCP4 data scaling version: (SCALA)