4UB1

DNA polymerase beta product complex with a templating adenine and 8-oxodGMP, 90 s


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829150 mM imidazole, 350 mM sodium chloride, 17% PEG3350, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.4249.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.131α = 90
b = 80.8β = 109.58
c = 55.462γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
12.3415097.30.05224.33.534952
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)
12.3412.39770.3342.32.5

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 3ISB2.34131.96233942338889.350.22780.22230.2772
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]
-8.6405-0.7204-2.04234.788
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d21.943
f_angle_d1.061
f_chiral_restr0.072
f_bond_d0.01
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2524
Nucleic Acid Atoms654
Solvent Atoms85
Heterogen Atoms2

Software

Software
Software NamePurpose
PHENIXrefinement