X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 1.5 M ammonium formate and 0.15 M sodium HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 318.9 α = 90
b = 349.3 β = 90
c = 368.4 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirror 1998-11-01
CCD NONIUS CAD4 mirror 1998-02-01
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 0.92 CHESS F1
SYNCHROTRON NSLS BEAMLINE X25 1.10 NSLS X25

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
2.7 50 92.8 0.114 -- -- 13.8 513239 513239 0.0 0.0 29.0
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)
2.7 2.8 82.7 0.212 -- 4.0 5.0 46826

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 2.7 50.0 -- 2.0 513239 494360 -- 89.0 0.216 -- 0.216 -- --
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 2.7 2.8 40374 0 40374 0.274 -- -- 73.1
X Ray Diffraction 2.8 2.91 44696 0 -- 0.2629 -- -- 81.0
X Ray Diffraction 2.91 3.2 95693 0 -- 0.2362 -- -- 86.6
X Ray Diffraction 3.2 3.66 101471 0 -- 0.214 -- -- 91.5
X Ray Diffraction 3.66 4.62 105457 0 -- 0.1893 -- -- 95.0
X Ray Diffraction 4.62 50.0 106669 0 -- 0.2039 -- -- 94.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 18.4
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.7
x_dihedral_angle_d 26.7
x_angle_deg 1.0
x_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6459
Nucleic Acid Atoms 0
Heterogen Atoms 21
Solvent Atoms 637

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR model building
SCALEPACK data reduction
DENZO data collection