X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbactch Under Paraffin Oil
pH 8
Temperature 289.0
Details PEG4000, sodium acetate, magnesium acetate, 3-bromopyruvate, pH 8.0, Microbactch under paraffin oil, temperature 289.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.31 α = 90
b = 129.04 β = 90
c = 166.16 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE -- 2000-06-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-ID

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
1.8 20 96.3 0.046 -- -- 4.84 142726 142726 -3.0 -3.0 18.2
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)
1.8 1.86 94.1 0.279 -- -- 4.8 13786

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
-- 1.8 19.86 0.0 2.0 142666 129143 12828 87.2 0.212 0.203 0.203 0.247 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 1.8 1.91 -- 2128 18882 0.283 0.338 0.007 86.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.1
Anisotropic B[1][1] 6.12
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.08
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.04
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.69
c_mcbond_it 1.23
c_scbond_it 1.87
c_angle_deg 1.6
c_scangle_it 2.52
c_bond_d 0.013
c_dihedral_angle_d 22.8
c_improper_angle_d 1.13
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13232
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 1016

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
SCALEPACK data reduction
DENZO data collection
CNS version: 1.0 refinement
AMORE model building