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Binary Complex of Human DNA Polymerase Mu with Mn8oxodGTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.827 α = 90 b = 122.827 β = 90 c = 49.859 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 30 99.9 0.06 0.999 25.9 13.32 21351
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.28 99.8 0.364 0.979 5.78 13.88
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.15 30 20288 1064 99.88 0.21509 0.21292 0.2152 0.25623 0.2553 RANDOM 54.307
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.93 r_dihedral_angle_4_deg 19.467 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_1_deg 5.558 r_long_range_B_refined 5.112 r_long_range_B_other 5.107 r_scangle_other 2.962 r_mcangle_it 2.61 r_mcangle_other 2.61 r_scbond_it 1.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.93 r_dihedral_angle_4_deg 19.467 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_1_deg 5.558 r_long_range_B_refined 5.112 r_long_range_B_other 5.107 r_scangle_other 2.962 r_mcangle_it 2.61 r_mcangle_other 2.61 r_scbond_it 1.856 r_scbond_other 1.854 r_mcbond_it 1.628 r_mcbond_other 1.627 r_angle_refined_deg 1.437 r_angle_other_deg 0.921 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing