X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 280.0
Details PEG 4000, magnesium chloride, tris buffer, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 280K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.18 α = 90
b = 72.18 β = 90
c = 142.78 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- --
CCD MARRESEARCH -- 2001-03-20
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --
SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 0.9800, 0.9811, 0.9500, 1.05 MPG/DESY, HAMBURG BW6

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 14.52 -- 0.039 -- -- -- 37955 37955 -- 0.0 22.2

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
-- 1.75 14.52 -- 0.0 37955 37955 3771 97.6 -- 0.2161 0.216 0.25 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 -- 642 5704 0.248 0.272 0.011 99.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.0
Anisotropic B[1][1] 0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.05
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.83
c_bond_d 0.005
c_angle_deg 1.3
c_dihedral_angle_d 22.9
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.09
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2353
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 393

Software

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