6AK8

Pre-catalytic Ternary Complex of Human DNA Polymerase Mu with Templating Adenine and Incoming Ca-8oxodGTP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1 M HEPES pH 7.5, 18% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.6854.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.75α = 90
b = 68.548β = 90
c = 110.165γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252018-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.745099.30.9786.616.6547246
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.84960.9122.046.45

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 REPLACEMENTTHROUGHOUT1.745044825236499.170.175340.174010.20082RANDOM26.93
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]
1.05-1.840.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.977
r_dihedral_angle_4_deg18.576
r_dihedral_angle_3_deg11.657
r_dihedral_angle_1_deg5.183
r_long_range_B_refined4.703
r_long_range_B_other4.702
r_scangle_other2.543
r_mcangle_it2.059
r_mcangle_other2.059
r_scbond_it1.611
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.977
r_dihedral_angle_4_deg18.576
r_dihedral_angle_3_deg11.657
r_dihedral_angle_1_deg5.183
r_long_range_B_refined4.703
r_long_range_B_other4.702
r_scangle_other2.543
r_mcangle_it2.059
r_mcangle_other2.059
r_scbond_it1.611
r_scbond_other1.611
r_angle_refined_deg1.438
r_mcbond_it1.351
r_mcbond_other1.351
r_angle_other_deg1.006
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2559
Nucleic Acid Atoms344
Solvent Atoms393
Heterogen Atoms57

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing