X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 298.0
Details 1M 1,6-hexanediol, 100 mM cobalt chloride, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.86 α = 90
b = 86.86 β = 90
c = 81.78 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-12-04
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 0.98 SSRL BL9-1

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
1.6 20 99.0 0.071 -- -- 4.6 45763 32506 0.0 -3.0 24.5
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)
1.6 1.63 99.0 0.46 -- 3.1 3.1 2264

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
MIR 1.6 20.0 0.0 0.0 45700 45700 4637 98.8 0.236 0.234 0.234 0.253 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 1.6 1.7 -- 761 6843 0.296 0.315 0.011 99.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.7
Anisotropic B[1][1] -3.75
Anisotropic B[1][2] 0.21
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 7.51
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.84
c_dihedral_angle_d 19.7
c_scangle_it 3.29
c_angle_deg 1.0
c_mcbond_it 1.14
c_scbond_it 2.15
c_bond_d 0.011
c_mcangle_it 1.79
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 3.5
Luzzati ESD (R-Free Set) 0.25
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2382
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 218

Software

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