X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 277.0
Details 12% PEG 3350, 0.1M magnesium acetate, 10mM Cobalt hexamine chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.43 α = 90
b = 68.43 β = 90
c = 243.66 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm mirrors 2002-03-01
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8000 SPring-8 BL41XU

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
2.5 30 97.1 0.054 -- -- 10.5 -- 20541 -- -- 49.1
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)
2.5 2.59 97.2 0.24 -- 16.0 -- --

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 2.5 28.26 -- 3.0 -- 20294 1993 96.6 -- 0.247 0.247 0.29 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 2.5 2.66 -- 322 2916 0.324 0.421 0.023 95.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 54.8
Anisotropic B[1][1] -7.77
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.77
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 15.53
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 4.86
c_scbond_it 7.02
c_angle_deg 1.4
c_bond_d 0.009
c_dihedral_angle_d 25.6
c_improper_angle_d 1.12
c_mcangle_it 7.01
c_scangle_it 9.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.44
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3307
Nucleic Acid Atoms 732
Heterogen Atoms 7
Solvent Atoms 144

Software

Software
Software Name Purpose
DENZO data reduction
CNS refinement
SCALEPACK data scaling
CNS phasing