X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.6
Details PROTEIN WAS CRYSTALLIZED FROM 22.5% PEG 4000, 100 MM CHES,, pH 8.60

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.54 α = 90
b = 61.54 β = 90
c = 60.88 γ = 120
Symmetry
Space Group P 31

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS V -- 2003-05-15
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
1.23 50 99.7 0.023 -- -- 4.1 -- 74888 -- 2.0 10.3
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)
1.23 1.27 99.5 0.19 -- 10.3 4.1 --

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 1.23 50.0 -- 0.0 -- 73570 7418 98.0 -- 0.178 0.178 0.196 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 1.23 1.31 -- 1162 10764 0.209 0.226 0.007 95.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 15.2
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.35
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.16
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.32
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.82
c_scbond_it 2.64
c_dihedral_angle_d 23.4
c_mcangle_it 1.62
c_angle_deg 1.2
c_bond_d 0.005
c_mcbond_it 1.23
c_scangle_it 3.71
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.13
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.14
Luzzati Sigma A (R-Free Set) 0.08
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1972
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 419

Software

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