X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.3
Details PROTEIN WAS CRYSTALLIZED FROM 1.1M LISULF, 100 MM MES, PH 6.25.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.71 α = 90
b = 115.71 β = 90
c = 115.66 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU IMAGE PLATE -- 2002-12-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL26B1 -- SPring-8 BL26B1

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
1.5 50 99.3 0.04 -- -- 10.3 -- 47654 -- 2.0 19.5
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)
1.5 1.55 98.3 0.359 -- 8.0 9.8 --

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 1.5 37.8 -- 0.0 -- 47263 4761 99.2 -- 0.196 0.196 0.201 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 1.5 1.59 -- 750 6974 0.319 0.309 0.011 98.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 26.2
Anisotropic B[1][1] -1.27
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.27
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.54
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 6.65
c_dihedral_angle_d 21.7
c_improper_angle_d 0.72
c_scbond_it 4.65
c_bond_d 0.005
c_angle_deg 1.1
c_mcbond_it 2.74
c_mcangle_it 3.93
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.19
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1209
Nucleic Acid Atoms 0
Heterogen Atoms 37
Solvent Atoms 162

Software

Software
Software Name Purpose
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling
CNS phasing