X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 300.5
Details 14% (w/v) PEG8000, 100mM Na-cacodylate, 400mM lithium sulfate, 80mM magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 131.18 α = 90
b = 131.18 β = 90
c = 204.05 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
CCD ADSC QUANTUM 4 -- 2002-02-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4

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
3.1 50 99.7 -- 0.117 -- 16.6 -- 19354 -- -3.0 --
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)
3.1 3.21 100.0 -- 0.602 6.2 15.9 1886

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
SIRAS 3.1 49.63 -- 0.0 -- 19309 992 99.4 -- -- 0.229 0.267 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 3.1 3.29 -- 162 2875 0.298 0.383 0.03 95.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 97.6
Anisotropic B[1][1] -12.72
Anisotropic B[1][2] 4.68
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.72
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 25.45
RMS Deviations
Key Refinement Restraint Deviation
c_mcbond_it 3.68
c_bond_d 0.006
c_scangle_it 8.28
c_dihedral_angle_d 16.5
c_improper_angle_d 1.26
c_mcangle_it 6.52
c_scbond_it 4.68
c_angle_deg 1.1
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.43
Luzzati Sigma A (R-Free Set) 0.45
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1726
Nucleic Acid Atoms 2751
Heterogen Atoms 7
Solvent Atoms 19

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SOLVE phasing
CNS refinement version: 1.1