5VS1

Human DNA polymerase beta pre-catalytic 8-oxoG:dA extension complex with dTTP bound in non-planar conformation


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
2.2645.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.6α = 90
b = 80.5β = 106.9
c = 55.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-02-17MSINGLE 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
12.552.9196.40.0520.0710.99712.961.97627883-345.504
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)
12.52.695.30.3910.5320.7462.31.96

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 REPLACEMENTTHROUGHOUT4rpx2.552.911376172598.020.21370.21060.2721RANDOM38.657
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]
0.45-0.831.68-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.517
r_dihedral_angle_3_deg16.494
r_dihedral_angle_4_deg14.123
r_dihedral_angle_1_deg5.711
r_angle_refined_deg1.417
r_angle_other_deg0.912
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.517
r_dihedral_angle_3_deg16.494
r_dihedral_angle_4_deg14.123
r_dihedral_angle_1_deg5.711
r_angle_refined_deg1.417
r_angle_other_deg0.912
r_chiral_restr0.069
r_bond_refined_d0.009
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 Atoms2572
Nucleic Acid Atoms634
Solvent Atoms50
Heterogen Atoms41

Software

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