4RQ6

Human DNA Polymerase Beta With Gapped DNA Containing an 8-oxo-7,8-dihydro-Guanine(8-oxoG) and dATP soaked with MgCl2 for 80 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
2.1943.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.41α = 90
b = 80.45β = 107.75
c = 55.68γ = 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
12.2544.2898.80.0828.73.719914
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)
12.252.32980.54223.56458

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 REPLACEMENTTHROUGHOUT2.2544.281890099198.530.20040.197660.25204RANDOM44.391
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]
0.06-0.040.09-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.648
r_dihedral_angle_4_deg15.541
r_dihedral_angle_3_deg14.409
r_long_range_B_refined6.6
r_long_range_B_other6.597
r_dihedral_angle_1_deg5.433
r_scangle_other4.489
r_mcangle_other3.502
r_mcangle_it3.5
r_scbond_it2.698
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.648
r_dihedral_angle_4_deg15.541
r_dihedral_angle_3_deg14.409
r_long_range_B_refined6.6
r_long_range_B_other6.597
r_dihedral_angle_1_deg5.433
r_scangle_other4.489
r_mcangle_other3.502
r_mcangle_it3.5
r_scbond_it2.698
r_scbond_other2.698
r_mcbond_it2.156
r_mcbond_other2.147
r_angle_refined_deg1.232
r_angle_other_deg0.846
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms2613
Nucleic Acid Atoms654
Solvent Atoms71
Heterogen Atoms18

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling