6IPH

Binary Complex of Human DNA Polymerase Mu with MndATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1 M HEPES pH 7.5, 1.5 M Li2SO4
Crystal Properties
Matthews coefficientSolvent content
2.4549.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.582α = 90
b = 124.582β = 90
c = 50.548γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1NSRRCTPS 05A

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
11.653099.50.0870.99714.997.9948180
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)
11.651.75990.3820.9544.258.03

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 REPLACEMENTTHROUGHOUT1.653045679248399.50.1890.187510.2156RANDOM24.855
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]
0.080.08-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.341
r_dihedral_angle_4_deg19.659
r_dihedral_angle_3_deg10.857
r_dihedral_angle_1_deg4.934
r_long_range_B_refined4.842
r_long_range_B_other4.576
r_scangle_other1.948
r_mcangle_it1.476
r_mcangle_other1.476
r_angle_refined_deg1.358
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.341
r_dihedral_angle_4_deg19.659
r_dihedral_angle_3_deg10.857
r_dihedral_angle_1_deg4.934
r_long_range_B_refined4.842
r_long_range_B_other4.576
r_scangle_other1.948
r_mcangle_it1.476
r_mcangle_other1.476
r_angle_refined_deg1.358
r_scbond_it1.215
r_scbond_other1.175
r_angle_other_deg0.904
r_mcbond_it0.884
r_mcbond_other0.884
r_chiral_restr0.078
r_bond_refined_d0.009
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 Atoms2585
Nucleic Acid Atoms
Solvent Atoms336
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing