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Binary complex of human DNA Polymerase Mu with MnATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LZD
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 2.47 50.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.989 α = 90 b = 124.989 β = 90 c = 50.618 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 MX300-HS 2018-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1.0 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.72 30 99.9 0.015 48.8 14.1 43294
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.78 100 0.093 8.3 13.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LZD 1.72 30 41058 2180 99.81 0.19299 0.19146 0.22215 0.2451 RANDOM 20.151
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] -0.04 -0.04 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.45 r_dihedral_angle_4_deg 20.199 r_dihedral_angle_3_deg 11.87 r_long_range_B_refined 5.17 r_dihedral_angle_1_deg 4.98 r_long_range_B_other 4.948 r_scangle_other 1.546 r_angle_refined_deg 1.392 r_mcangle_it 1.231 r_mcangle_other 1.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.45 r_dihedral_angle_4_deg 20.199 r_dihedral_angle_3_deg 11.87 r_long_range_B_refined 5.17 r_dihedral_angle_1_deg 4.98 r_long_range_B_other 4.948 r_scangle_other 1.546 r_angle_refined_deg 1.392 r_mcangle_it 1.231 r_mcangle_other 1.231 r_scbond_it 0.947 r_scbond_other 0.929 r_angle_other_deg 0.921 r_mcbond_it 0.71 r_mcbond_other 0.71 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 2579 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing