X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details 0.1 M BIS/TRIS, 0.2 M Ammonium Sulfate, 25 % PEG 3350, soaked with 10 mM UDP-N-Acetylglucosamine and 10 mM Mg(Cl)2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 93.66 α = 90
b = 93.66 β = 90
c = 275.9 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirrors 1998-04-25
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM1A 0.873 ESRF BM1A

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
1.96 30 98.0 -- 0.062 -- 2.4 81753 33249 0.0 0.0 19.1
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)
1.96 2.03 95.4 -- 0.311 3.6 2.4 3197

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
FOURIER SYNTHESIS 1.96 30.0 0.0 0.0 33249 33242 1658 98.0 -- -- 0.188 0.221 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 1.96 2.03 -- 155 3042 0.256 0.286 -- 91.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 27.2
Anisotropic B[1][1] -2.699
Anisotropic B[1][2] -6.737
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.699
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.399
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 5.0
c_scbond_it 3.5
c_mcangle_it 2.1
c_mcbond_it 1.4
c_improper_angle_d 1.0
c_dihedral_angle_d 25.6
c_angle_deg 1.3
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3360
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 482

Software

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