X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 294.0
Details PEG 8000, glycerol, bis-tris, magnesium chloride, dithiothreitol, 2-aza-2,3-dihydrogeranyl diphosphate , pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 198.38 α = 90
b = 198.38 β = 90
c = 122.84 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2002-04-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.900 APS 14-BM-C

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
3.1 30 100.0 -- 0.087 -- 33.0 26476 26476 -- -- --
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)
3.1 3.21 99.8 -- 0.215 13.6 10.2 2585

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 3.1 29.93 -- 0.0 26301 26300 2072 100.0 -- 0.207 0.207 0.233 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 3.1 3.29 -- 311 3964 0.253 0.326 0.019 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 42.5
Anisotropic B[1][1] 1.72
Anisotropic B[1][2] 2.95
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.43
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.006
c_dihedral_angle_d 19.2
c_improper_angle_d 0.78
c_scangle_it 16.25
c_mcangle_it 11.58
c_angle_deg 1.2
c_mcbond_it 7.45
c_scbond_it 11.09
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.39
Luzzati Sigma A (R-Free Set) 0.52
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4405
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 26

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.0