2D3Y

Crystal structure of uracil-DNA glycosylase from Thermus Thermophilus HB8


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES, 11.5% PEG3350, 0.2M Ammonium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.94488936.757332

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.18α = 90
b = 62.35β = 90
c = 63.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2004-06-15MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 2102004-05-27MMAD
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU0.9797SPring-8BL45XU
2SYNCHROTRONSPRING-8 BEAMLINE BL44B20.97940,0.97280,0.9815,0.9791SPring-8BL44B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,21.55500970.08533.24.72745327453-39.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.551.6198.10.29710.24.72719

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1.555027421269922696950.1860.21random11.2
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.021.19-1.18
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23
c_improper_angle_d2.73
c_scangle_it2.58
c_scbond_it1.7
c_mcangle_it1.32
c_angle_deg1.3
c_mcbond_it0.85
c_bond_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1715
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms36

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement
HKL-2000data reduction