X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 295.0
Details 2.78M Ammonium sulphate, 100mM K2HPO4, 3%(v/v) Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.29 α = 90
b = 85.29 β = 90
c = 77.13 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2008-10-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
2.05 33.31 95.1 0.07 -- -- 1.64 -- 13123 -- -- --
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)
2.05 2.12 93.2 0.244 -- 1.8 1.64 2454

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 2.05 33.31 -- 0.0 -- 13122 655 99.8 -- -- 0.205 0.249 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 2.05 2.12 -- 59 1257 0.307 0.424 0.055 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.2186
Anisotropic B[1][1] 2.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.35
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.7
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.4
c_scangle_it 2.8
c_bond_d 0.007
c_mcbond_it 1.38
c_dihedral_angle_d 23.6
c_scbond_it 1.96
c_improper_angle_d 0.88
c_mcangle_it 2.17
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1502
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 172

Software

Software
Software Name Purpose
d*TREK data scaling version: 7.1SSI
d*TREK data reduction version: 7.1SSI
MOLREP phasing
CNS refinement version: 1.2
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
CrystalClear data reduction
CrystalClear data scaling