X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.3
Temperature 295.0
Details PEG 550 monomethylether, glycerol, sodium chloride, magnesium acetate, bicine, tris buffer, dithiothreitol, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 137.2 α = 90
b = 137.2 β = 90
c = 40.07 γ = 120
Symmetry
Space Group P 64 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 mirrors 2001-04-20
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.909 CHESS A1

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
2.6 50 99.9 0.052 -- -- 12.0 7229 7221 2.0 2.0 82.3
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)
2.6 2.69 99.9 0.217 -- 9.14 8.2 708

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 using a specially built model 2.7 44.91 0.0 0.0 6469 6469 508 99.6 0.2551 0.2551 0.2523 0.2889 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 2.7 2.8 617 49 568 0.3295 0.3353 0.04 --
X Ray Diffraction 2.8 2.91 621 45 -- 0.3134 0.3547 -- --
X Ray Diffraction 2.91 3.04 636 53 -- 0.2986 0.3658 -- --
X Ray Diffraction 3.04 3.2 628 49 -- 0.2696 0.3673 -- --
X Ray Diffraction 3.2 3.4 636 50 -- 0.2628 0.277 -- --
X Ray Diffraction 3.4 3.66 644 60 -- 0.297 0.2816 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 93.4
Anisotropic B[1][1] 2.22
Anisotropic B[1][2] 15.96
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.43
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.64
c_dihedral_angle_d 15.6
c_angle_deg 1.0
c_bond_d 0.007
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.41
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 892
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 27

Software

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