X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 294.0
Details PEG 4000, HEPES, sodium chloride, glycerol, spermine tetrahydrochloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.25 α = 90
b = 74.25 β = 90
c = 215.8 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 -- 2001-04-02
Diffraction Radiation
Monochromator Protocol
Si 111 Channel SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 0.978 NSLS X8C

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
3 19.9 85.5 -- -- -- -- 48246 10900 7.0 5.0 --
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)
3.0 3.19 97.0 -- -- -- -- --

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 3.0 19.99 -- 7.0 48246 10900 809 85.5 0.28 -- 0.26 0.339 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 3.0 3.19 1200 96 1185 0.281 0.36 0.037 62.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 28.0
Anisotropic B[1][1] 10.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 10.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -21.41
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 1.73
c_scbond_it 1.15
c_mcangle_it 1.56
c_mcbond_it 0.92
c_improper_angle_d 0.89
c_dihedral_angle_d 22.9
c_angle_deg 1.5
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 7.0
Luzzati ESD (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3309
Nucleic Acid Atoms 0
Heterogen Atoms 86
Solvent Atoms 0

Software

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