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_scangle_it 8.28
c_scbond_it 4.68
c_mcangle_it 6.52
c_mcbond_it 3.68
c_improper_angle_d 1.26
c_dihedral_angle_d 16.5
c_angle_deg 1.1
c_bond_d 0.006
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SOLVE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
SOLVE model building
SCALEPACK data reduction
DENZO data collection