4PGX

Structure of human DNA polymerase beta complexed with G in the template base paired with incoming non-hydrolyzable TTP and MANGANESE


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29814%?23% PEG3400, and 350 mM sodium acetate in 50 mM imidazole (pH 7.5)
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.969α = 90
b = 79.796β = 107.37
c = 55.635γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.30.97648ALS5.0.3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.07720100215.62554224.46

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 DIFFRACTIONNONE2.07719.9724599125295.630.18540.18320.2265
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_d19.591
f_angle_d1.078
f_chiral_restr0.075
f_bond_d0.004
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2608
Nucleic Acid Atoms632
Solvent Atoms162
Heterogen Atoms33

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
HKL-2000data reduction
PDB_EXTRACTdata extraction