5VS3

Human DNA polymerase beta 8-oxoG:dA extension with dTTP after 90 s


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RPX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29350 mM imidazole pH 7.0-7.5, 350 mM sodium acetate, 16-18% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.244.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.4α = 90
b = 79.6β = 107.1
c = 55.2γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2015-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.752.7694.90.0390.0540.99813.071.93385729-329.646
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.996.90.3590.4980.832.281.937

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-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4rpx1.752.7642694224898.040.20840.20620.2487RANDOM27.439
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]
-0.290.22-0.010.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.77
r_dihedral_angle_3_deg13.065
r_dihedral_angle_4_deg12.305
r_dihedral_angle_1_deg5.172
r_angle_refined_deg1.355
r_angle_other_deg1.244
r_chiral_restr0.091
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.77
r_dihedral_angle_3_deg13.065
r_dihedral_angle_4_deg12.305
r_dihedral_angle_1_deg5.172
r_angle_refined_deg1.355
r_angle_other_deg1.244
r_chiral_restr0.091
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2601
Nucleic Acid Atoms654
Solvent Atoms337
Heterogen Atoms57

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing
XDSdata reduction