4UB3

DNA polymerase beta closed product complex with a templating cytosine and 8-oxodGMP, 60 s


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FMSPDB entry 2FMS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829150 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2344.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.698α = 90
b = 80.094β = 107.8
c = 55.358γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442013-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.065097.40.08316.34.727186
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)
12.062.1391.20.5112.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 2FMS2.0621.34321786108683.080.21710.21410.2744
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]
4.87034.2122-1.69-3.1917
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.481
f_angle_d1.073
f_chiral_restr0.056
f_bond_d0.014
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2588
Nucleic Acid Atoms652
Solvent Atoms173
Heterogen Atoms12

Software

Software
Software NamePurpose
PHENIXrefinement