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_scangle_it 16.25
c_scbond_it 11.09
c_mcangle_it 11.58
c_mcbond_it 7.45
c_improper_angle_d 0.78
c_dihedral_angle_d 19.2
c_angle_deg 1.2
c_bond_d 0.006
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

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