6AK9

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


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
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.907α = 90
b = 68.742β = 90
c = 110.211γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2018-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9301000.03621.75.236204
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.971000.1973.95.2

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 REPLACEMENTTHROUGHOUT1.913034340178899.560.166990.165120.20361RANDOM21.043
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]
0.05-0.070.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.955
r_dihedral_angle_4_deg17.932
r_dihedral_angle_3_deg11.341
r_dihedral_angle_1_deg5.213
r_long_range_B_refined4.56
r_long_range_B_other4.226
r_scangle_other2.127
r_mcangle_it1.86
r_mcangle_other1.86
r_angle_refined_deg1.435
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.955
r_dihedral_angle_4_deg17.932
r_dihedral_angle_3_deg11.341
r_dihedral_angle_1_deg5.213
r_long_range_B_refined4.56
r_long_range_B_other4.226
r_scangle_other2.127
r_mcangle_it1.86
r_mcangle_other1.86
r_angle_refined_deg1.435
r_scbond_other1.295
r_scbond_it1.294
r_mcbond_it1.132
r_mcbond_other1.131
r_angle_other_deg0.992
r_chiral_restr0.075
r_bond_refined_d0.008
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 Atoms2556
Nucleic Acid Atoms342
Solvent Atoms384
Heterogen Atoms59

Software

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