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 = 86.56 α = 90
b = 86.56 β = 90
c = 81.36 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-09-29
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.00 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
1.8 20 89.5 0.058 -- -- 2.7 29025 29025 0.0 -3.0 34.4
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)
1.8 1.86 79.8 0.366 -- 2.7 1.8 2569

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 1.8 20.0 0.0 0.0 28768 28768 2865 89.7 0.2372 0.234 0.234 0.266 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 1.8 1.91 -- 435 3816 0.307 0.322 0.015 80.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.7
Anisotropic B[1][1] -4.21
Anisotropic B[1][2] 1.37
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.42
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 19.9
c_mcangle_it 0.94
c_improper_angle_d 0.82
c_scangle_it 1.15
c_bond_d 0.01
c_angle_deg 1.1
c_mcbond_it 0.52
c_scbond_it 0.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.23
Luzzati Resolution Cutoff (Low) 3.5
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2373
Nucleic Acid Atoms 0
Heterogen Atoms 32
Solvent Atoms 185

Software

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