X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 291.0
Details 1.68 M ammonium sulphate, 10 mM N-acetyl-glucosamine-6-phosphate and 0.1 mM 2-deoxy-2-amino D-glucitol 6-phosphate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.88 α = 90
b = 110.89 β = 90
c = 180.88 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-03-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.78 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
1.75 19.97 94.3 -- 0.052 -- 3.8 221759 209143 1.0 0.0 19.5
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)
1.75 1.86 95.8 -- 0.224 3.4 3.6 32182

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 1.75 19.97 -- 0.0 221759 209143 20802 94.3 0.1954 0.1954 0.193 0.217 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 1.75 1.76 4218 436 31921 0.1929 0.216 0.004 96.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 25.9
Anisotropic B[1][1] -1.76
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 6.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.59
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 0.98
c_scangle_it 2.62
c_scbond_it 1.77
c_angle_deg 1.4
c_bond_d 0.005
c_dihedral_angle_d 23.1
c_improper_angle_d 0.85
c_mcangle_it 1.47
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13436
Nucleic Acid Atoms 0
Heterogen Atoms 383
Solvent Atoms 2194

Software

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