X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 17.0
Details NaMES, MPD, N-acetyl-beta-D-glycopyranosylamine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 17K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 124 α = 90
b = 124 β = 90
c = 122.28 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS II -- 1998-02-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2.4 30 99.4 0.047 -- -- 5.3 82210 81720 0.0 -2.0 26.9
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)
2.4 2.49 97.8 0.174 -- -- 2.0 --

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
MOLECULAR REPLACEMENT 2.4 30.0 0.0 0.0 81964 78076 7804 95.1 -- 0.198 0.198 0.235 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 2.4 2.55 -- 1183 10520 0.268 0.283 0.008 85.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.2
Anisotropic B[1][1] -2.72
Anisotropic B[1][2] 0.99
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.43
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.52
c_mcbond_it 2.58
c_dihedral_angle_d 24.8
c_bond_d 0.012
c_scangle_it 5.78
c_scbond_it 4.02
c_angle_deg 2.0
c_mcangle_it 3.95
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.28
Luzzati Sigma A (Observed) 0.32
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12854
Nucleic Acid Atoms 0
Heterogen Atoms 60
Solvent Atoms 255

Software

Software
Software Name Purpose
CNS refinement
DENZO data reduction
SCALEPACK data scaling
CNS phasing