5VI0

Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an abasic site analog


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5294.15100 mM Tris-HCl, pH 8.5, 18% PEG4000, 5% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.7154.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.636α = 90
b = 94.935β = 90
c = 134.03γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294CCDMARMOSAIC 225 mm CCD2015-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.3965099.70.1090.1150.0367.99.84102925.19
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4999.80.4290.4520.140.9549.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE2.39640.42440519197398.50.17070.16790.22525.8878
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.885
f_angle_d0.967
f_chiral_restr0.049
f_bond_d0.008
f_plane_restr0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5685
Nucleic Acid Atoms870
Solvent Atoms529
Heterogen Atoms46

Software

Software
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing