X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 293.0
Details 0.1M Bicin, 5% v/v Glycerol, 10% w/v PEG8000, 4% v/v Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.63 α = 90
b = 68.63 β = 90
c = 86.4 γ = 90
Symmetry
Space Group P 41

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2004-03-25
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 2.29 -- --
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.00000 SPring-8 BL44B2

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
1.88 31.9 99.5 -- -- -- 7.53932 -- 32500 -- -3.0 28.3
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)
1.88 1.95 100.0 -- 0.66 -- -- --

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
SAD 1.88 31.89 -- 0.0 -- 32440 1609 99.4 -- 0.2 0.2 0.227 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 1.88 2.0 -- 327 5093 0.244 0.275 0.015 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 41.8
Anisotropic B[1][1] 3.21
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.41
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 2.12
c_mcbond_it 1.38
c_improper_angle_d 0.95
c_scbond_it 2.08
c_bond_d 0.008
c_dihedral_angle_d 22.6
c_scangle_it 3.16
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.22
Luzzati Sigma A (Observed) 0.15
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2353
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 178

Software

Software
Software Name Purpose
CNS refinement version: 1.1
HKL-2000 data reduction
SCALEPACK data scaling
SOLVE phasing