4F5P

Open ternary mismatch complex of R283K DNA polymerase beta with a dATP analog


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829150mM Imidazole, 350mM Sodium Acetate, 19% PEG3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3948.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.38α = 90
b = 79.24β = 105.49
c = 54.88γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 92Mirrors2011-09-25MSINGLE 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
11.852899.70.0494.9185280185280-3
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)
11.851.9297.20.3672.342.2

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 (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT3ISB1.8522.1093629236292366393.860.20710.20280.2452
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]
2.41385.4155-3.18880.775
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.258
f_angle_d1.231
f_chiral_restr0.101
f_bond_d0.01
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2580
Nucleic Acid Atoms632
Solvent Atoms292
Heterogen Atoms33

Software

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