X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.8
Temperature 291.0
Details HEPES, sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP at 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.68 α = 90
b = 126.68 β = 90
c = 139.33 γ = 120
Symmetry
Space Group P 63 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MACSCIENCE DIP100S -- 1999-01-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-1 -- SSRL BL9-1

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
1.9 50 92.2 0.072 -- -- 3.4 48346 n/a 0.0 -- 24.8
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)
1.9 2.02 90.9 0.325 -- -- 2.9 7806

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
-- 1.9 50.0 -- 0.0 48346 48346 4880 92.1 -- -- 0.183 0.232 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 1.9 2.02 7041 765 7041 0.274 0.295 0.011 90.9
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.33
c_scbond_it 1.51
c_mcangle_it 1.56
c_mcbond_it 0.93
c_dihedral_angle_d 23.8
c_improper_angle_d 0.87
c_angle_deg 1.3
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.27
Luzzati Sigma A (R-Free Set) 0.24
Number Disordered Residues 0.0
Occupancy Sum Hydrogen 0.0
Occupancy Sum Non Hydrogen 2390.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2092
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 298

Software

Computing
Computing Package Purpose
MAR, DENZO Data Reduction (intensity integration)
CCP4 Data Reduction (data scaling)
CNS Structure Solution
CNS 0.5, SHELXL-97 Structure Refinement
Software
Software Name Purpose
SHELXL-97 refinement
CNS version: 0.5 refinement
CNS model building