4GXI

R283K DNA polymerase beta binary complex with a templating 8OG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ISB3isb.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829150mM imidazole, 350mM Sodium Acetate, 18% Peg3350, pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.797α = 90
b = 79.258β = 105.62
c = 54.365γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92mirrors2011-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
11.955098.30.11411.24.7-322.2
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)
11.952.0286.30.52.293.42802

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3isb.pdb1.94922.0972955429554293090.290.20830.20830.20260.2589random22.2
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]
-2.38411.64680.7871.5971
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.555
f_angle_d1.123
f_chiral_restr0.07
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2620
Nucleic Acid Atoms632
Solvent Atoms360
Heterogen Atoms4

Software

Software
Software NamePurpose
PHENIXrefinement
CNSrefinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing