7S9M

Crystal Structure of DNA Polymerase Beta with Ring open intermediate Fapy-dG base-paired with a dA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ISB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829114-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.550.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.303α = 90
b = 80.841β = 109.042
c = 56.507γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2021-01-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.312599.90.99710.834.32499137.57
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.316.270.388

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3ISB2.3124.871.3324991245461.750.2260.21820.299640.56
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_d24.9721
f_angle_d1.2305
f_chiral_restr0.2397
f_bond_d0.015
f_plane_restr0.0071
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms635
Solvent Atoms49
Heterogen Atoms8

Software

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