X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 292.0
Details 25% PEG 5000 monomethyl ether, 0.2M ammonium acetate, 0.1M cacodoylate, 150 mM Nacl, 50 mM imidazole (pH=6.5), 10 mM Manganese chloride, 5 mM beta-glycerophosphate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.77 α = 90
b = 108.77 β = 90
c = 72.67 γ = 90
Symmetry
Space Group I 4

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 277
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1998-01-09
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.2 40 94.9 0.087 -- -- 6.2 18385 18385 -- 0.0 10.7
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)
2.2 2.24 70.5 0.49 -- -- -- 138

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 2.2 30.0 -- 0.0 19965 18385 1580 92.2 -- -- 0.215 0.2483 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 2.2 2.28 -- 1208 1519 0.3981 0.4583 0.043 56.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 43.2
Anisotropic B[1][1] 1.61
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.22
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 4.59
c_mcbond_it 2.99
c_dihedral_angle_d 27.7
c_scbond_it 5.31
c_bond_d 0.008
c_angle_deg 1.5
c_scangle_it 7.25
c_improper_angle_d 0.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.57
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.58
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2404
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 75

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.0