X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Details CRYSTALLIZATION EXPERIMENTS WERE CONDUCTED IN HANGING DROPS CONTAINING 4.2 MG/ML E. COLI TS, 0.38 MM DUMP, 3.8 MM DTT, AND 1.2 M (NH4)2SO4, AT PH 7.8 (20 MM KPO4) SUSPENDED OVER A WELL SOLUTION CONTAINING 2.4 M (NH4)2SO4 AND 1.0 MM DTT., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 133.06 α = 90
b = 133.06 β = 90
c = 133.06 γ = 90
Symmetry
Space Group I 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU -- 1996-11
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
2.1 40 96.9 0.067 0.067 -- 7.1 -- 23029 -- 1.0 19.9
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)
2.1 2.18 91.5 0.319 0.319 3.4 4.7 --

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
DIFFERENCE FOURIER 2.2 8.0 -- 0.0 -- 18908 1862 96.5 -- 0.172 0.172 0.217 SHELLS
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 2.2 2.33 -- 279 2809 0.238 0.262 0.016 95.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.81
x_scbond_it 3.81
x_mcangle_it 3.74
x_mcbond_it 2.49
x_improper_angle_d 1.19
x_bond_d 0.008
x_angle_deg 1.5
x_dihedral_angle_d 25.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2153
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 113

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.843 Structure Solution
X-PLOR 3.843 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.843 refinement
X-PLOR version: 3.843 model building