X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 303.0
Details ammonium sulfate, PEG 400, NaCl, NaPO4, Pipes, Tris, 2-O-methyl-alpha-D-N-acetyl neuraminic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.03 α = 90
b = 48.03 β = 90
c = 130.4 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 ADSC QUANTUM 4 mirror 2001-03-02
Diffraction Radiation
Monochromator Protocol
bent G3(III) single crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C

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
1.4 30 99.5 0.05 -- -- 8.25 31002 31002 0.0 0.0 12.8
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)
1.4 1.43 98.3 0.251 -- 5.51 5.71 1993

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
SIR 1.4 25.0 -- 0.0 30898 30898 1530 99.5 -- -- 0.169 0.181 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 1.4 1.45 3037 142 2895 0.204 0.22 -- 99.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 14.5
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.292
c_scbond_it 2.521
c_mcangle_it 1.852
c_mcbond_it 1.294
c_improper_angle_d 1.25
c_dihedral_angle_d 27.1
c_angle_deg 1.86
c_bond_d 0.015
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.14
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.15
Luzzati Sigma A (R-Free Set) 0.07
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1273
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 190

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
CNS model building