X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 18 % PEG 400 (w/w), 300 mM CaCl2 50 mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 89.51 α = 90
b = 89.51 β = 90
c = 278.75 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-05-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 -- ESRF ID14-3

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
1.75 50 97.9 0.046 -- -- 2.3 84013 82248 -- 2.0 18.37
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)
1.75 1.8 96.4 0.354 5926.0 2.9 2.0 --

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 1.75 29.14 0.0 0.0 82248 82248 8308 97.7 0.183 0.183 0.183 0.219 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 1.75 1.86 -- 1375 12162 0.276 0.312 0.008 96.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.2
Anisotropic B[1][1] 2.02
Anisotropic B[1][2] 2.05
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.02
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.05
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.856
c_scbond_it 2.694
c_mcangle_it 2.287
c_mcbond_it 1.667
c_improper_angle_d 0.74
c_dihedral_angle_d 24.6
c_angle_deg 1.53
c_bond_d 0.011
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6930
Nucleic Acid Atoms 0
Heterogen Atoms 188
Solvent Atoms 694

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMORE model building