6IPF

Post-catalytic Complex of Human DNA Polymerase Mu with Templating Cytosine and Mn-8oxodGMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1 M HEPES pH 7.5, 18% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.4850.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.778α = 90
b = 68.792β = 90
c = 109.62γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252018-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.773099.70.0750.99812.825.5744400
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.8898.90.770.7942.135.68

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 REPLACEMENTTHROUGHOUT1.773042170226799.740.189620.188110.21818RANDOM34.539
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]
-0.31-1.381.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.79
r_dihedral_angle_4_deg18.544
r_dihedral_angle_3_deg11.899
r_long_range_B_refined5.21
r_long_range_B_other5.209
r_dihedral_angle_1_deg4.991
r_scangle_other3.106
r_mcangle_it2.577
r_mcangle_other2.576
r_scbond_it2.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.79
r_dihedral_angle_4_deg18.544
r_dihedral_angle_3_deg11.899
r_long_range_B_refined5.21
r_long_range_B_other5.209
r_dihedral_angle_1_deg4.991
r_scangle_other3.106
r_mcangle_it2.577
r_mcangle_other2.576
r_scbond_it2.008
r_scbond_other2.007
r_mcbond_it1.626
r_mcbond_other1.626
r_angle_refined_deg1.387
r_angle_other_deg0.991
r_chiral_restr0.07
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms2560
Nucleic Acid Atoms365
Solvent Atoms278
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing