X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details PEG1000, sodium cacodylate,0.5% glycerol, 0.2 mM HgCl2 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.87 α = 90
b = 67.87 β = 90
c = 340.47 γ = 120
Symmetry
Space Group P 65 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2004-12-22
Diffraction Radiation
Monochromator Protocol
Si [111], horizontally focussing SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.843 EMBL/DESY, Hamburg BW7B

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
2.1 25 99.3 0.075 -- -- 6.2 28370 28370 0.0 0.0 19.2
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)
2.1 2.22 97.1 0.342 -- 4.3 6.4 4317

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 2.1 25.0 -- 0.0 28370 28370 1382 99.3 0.237 0.212 0.212 0.247 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 2.1 2.23 4342 231 4342 0.31 0.347 0.023 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 38.2
Anisotropic B[1][1] -5.76
Anisotropic B[1][2] -0.13
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.76
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.51
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 4.42
c_scangle_it 5.21
c_angle_deg 1.5
c_mcbond_it 3.0
c_dihedral_angle_d 22.5
c_bond_d 0.009
c_improper_angle_d 1.57
c_mcangle_it 3.93
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.27
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 25.0
Luzzati ESD (R-Free Set) 0.32
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1742
Nucleic Acid Atoms 774
Heterogen Atoms 8
Solvent Atoms 163

Software

Software
Software Name Purpose
CNS refinement version: 1.1
XDS data reduction
XSCALE data scaling
CNS phasing