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Binary complex of human DNA Polymerase Mu with MndGTP
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 7.5 298 0.1 M HEPES pH 7.5, 1.5 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.45 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.719 α = 90 b = 124.719 β = 90 c = 50.509 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 MX300HE 2017-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.0 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 30 95.8 41.38 7.8 26362
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 98.1 5.34 7.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4LZD 2 25.407 25025 1283 95.68 0.20346 0.20153 0.2092 0.2406 0.2505 RANDOM 29.824
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] 0.06 0.06 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.285 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_3_deg 12.363 r_long_range_B_refined 5.238 r_dihedral_angle_1_deg 5.135 r_long_range_B_other 5.08 r_scangle_other 1.639 r_mcangle_it 1.532 r_mcangle_other 1.532 r_angle_other_deg 1.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.285 r_dihedral_angle_4_deg 17.059 r_dihedral_angle_3_deg 12.363 r_long_range_B_refined 5.238 r_dihedral_angle_1_deg 5.135 r_long_range_B_other 5.08 r_scangle_other 1.639 r_mcangle_it 1.532 r_mcangle_other 1.532 r_angle_other_deg 1.394 r_angle_refined_deg 1.339 r_scbond_it 0.981 r_scbond_other 0.92 r_mcbond_it 0.877 r_mcbond_other 0.877 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 2604 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing