7S9Q

Ternary complex of DNA Polymerase Beta with Template Fapy-dG and an incoming dATP analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C2M 

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
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.624α = 90
b = 78.583β = 112.435
c = 54.916γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2020-05-29MSINGLE 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
11.925990.9989.4143377224.2
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)
11.95.140.42

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-VALUE3C2M1.924.151.3628890200684.780.19680.1930.247428.02
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_d24.5076
f_angle_d0.7408
f_chiral_restr0.0428
f_bond_d0.0087
f_plane_restr0.0033
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2588
Nucleic Acid Atoms633
Solvent Atoms421
Heterogen Atoms38

Software

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