4RQ8

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MnCl2 for 35 s


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829550 MM IMIDAZOLE, 350 MM SODIUM Acetate, 17% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1643.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.22α = 90
b = 82.54β = 110.89
c = 54.74γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193CCDRAYONIX MX225HE2014-07-23MSINGLE 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)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
1241.2799.50.1253.428117
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)
122.1198.70.4992.43.212924

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT240.7926717137899.430.210030.206880.27049RANDOM28.409
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]
0.01-0.320.160.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.706
r_dihedral_angle_3_deg14.758
r_dihedral_angle_4_deg10.964
r_dihedral_angle_1_deg5.38
r_long_range_B_refined5.05
r_long_range_B_other5.007
r_scangle_other3.222
r_mcangle_it2.497
r_mcangle_other2.496
r_scbond_it1.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.706
r_dihedral_angle_3_deg14.758
r_dihedral_angle_4_deg10.964
r_dihedral_angle_1_deg5.38
r_long_range_B_refined5.05
r_long_range_B_other5.007
r_scangle_other3.222
r_mcangle_it2.497
r_mcangle_other2.496
r_scbond_it1.986
r_scbond_other1.986
r_mcbond_it1.547
r_mcbond_other1.543
r_angle_refined_deg1.359
r_angle_other_deg0.871
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2682
Nucleic Acid Atoms654
Solvent Atoms231
Heterogen Atoms54

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling