6IPJ

Binary Complex of Human DNA Polymerase Mu with MndTTP


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
2.4549.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.544α = 90
b = 124.544β = 90
c = 50.566γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2018-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.983099.80.0540.01644.71128285
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.051000.750.2253.6910.8

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 REPLACEMENTTHROUGHOUT1.983026800140099.570.199890.197670.23955RANDOM27.72
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]
0.090.09-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg20.085
r_dihedral_angle_3_deg12.986
r_dihedral_angle_1_deg5.352
r_long_range_B_refined4.789
r_long_range_B_other4.593
r_scangle_other1.881
r_mcangle_it1.518
r_mcangle_other1.517
r_scbond_it1.405
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg20.085
r_dihedral_angle_3_deg12.986
r_dihedral_angle_1_deg5.352
r_long_range_B_refined4.789
r_long_range_B_other4.593
r_scangle_other1.881
r_mcangle_it1.518
r_mcangle_other1.517
r_scbond_it1.405
r_scbond_other1.404
r_angle_refined_deg1.398
r_angle_other_deg0.915
r_mcbond_it0.88
r_mcbond_other0.88
r_chiral_restr0.078
r_bond_refined_d0.01
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 Atoms2594
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing