X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Batch Method
pH 9
Temperature 293.0
Details Protein Solution (20mg/ml protein in 0.02M Tris.HCl pH9.0) mixed with mother liquor (3.2M Ammonium Sulphate, 0.05M Tris.HCl, pH9.0) for final concentrations of 2.5M Ammonium Sulphate, Batch Method, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.32 α = 90
b = 90.32 β = 90
c = 45.23 γ = 120
Symmetry
Space Group P 6

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2008-08-21
Diffraction Radiation
Monochromator Protocol
Multilayer 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
1.54 45.16 79.6 0.04 -- -- 3.9 31218 24865 -- 3.0 15.0
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)
1.54 1.6 18.2 0.118 -- 3.9 1.26 566

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
FOURIER SYNTHESIS 1.7 45.16 -- 0.0 22372 22079 1066 94.5 -- -- 0.214 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 1.7 1.81 2862 152 -- 0.247 0.279 0.022 77.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Restrained
Mean Isotropic B 16.792
Anisotropic B[1][1] -0.513
Anisotropic B[1][2] -1.174
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.513
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.027
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_improper_angle_d 0.77
c_dihedral_angle_d 17.8
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.02
Luzzati Sigma A (Observed) 0.06
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1223
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 323

Software

Software
Software Name Purpose
d*TREK data processing version: 9.9.3L
CNS refinement version: 1.1
PDB_EXTRACT data extraction version: 3.005
CrystalClear data collection
CrystalClear data reduction
d*TREK data scaling
CNS phasing