X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.9
Temperature 293.0
Details 4 ul hanging drops were prepared by mixing equal volumes of protein (10 mg/ml in 20 mM HEPES, pH 7.0) and reservoir solution. The drops equilibrated against 500 ul of 15-18% PEG6000, 0.1M sodium citrate, pH 5.9, 20 mM L-cysteine, and 5% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.2 α = 90
b = 83.3 β = 90
c = 96 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-01-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B -- NSLS X12B

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
2.8 50 96.6 0.174 -- -- 4.5 7014 6775 0.0 2.0 47.0
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)
2.8 2.9 82.4 0.267 -- -- 3.0 692

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
-- 2.8 40.0 -- 0.0 7014 6386 687 92.3 -- -- 0.2 0.285 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 2.8 2.9 -- 84 824 0.28 0.345 0.038 80.4
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.25
c_scbond_it 2.29
c_mcangle_it 2.5
c_mcbond_it 1.56
c_improper_angle_d 0.89
c_bond_d 0.013
c_angle_deg 1.7
c_dihedral_angle_d 25.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.42
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1922
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 45

Software

Computing
Computing Package Purpose
MAR, DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.851, CNS Structure Refinement
Software
Software Name Purpose
XPLOR version: 3.851 & CNS refinement
AMORE model building
DENZO/SCALEPACK data reduction
MAR data collection