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KOD-H4 DNA polymerase mutant in a ternary complex with DNA/DNA and non-hydrolyzable triphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 Morpheus II condition A1: 36 % v/v of a 72% mix: 30% w/v PEG 3000, 40% v/v 1, 2, 4-Butanetriol, 2% w/v NDSB 256; 0.03 M Lithium sulfate, 0.03 M Sodium sulfate, 0.03 Potassium sulfate, 0.1 M MOPSO/Bis-Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.99 58.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.97 α = 90 b = 152.462 β = 90 c = 70.125 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS EIGER X 16M 2023-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 46.796 99.4 0.985 3.75 3 95588
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.49 0.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.35 38.58 1.07 93177 3647 96.93 0.2383 0.2368 0.2363 0.2755 0.2759
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.398 f_angle_d 0.628 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6200 Nucleic Acid Atoms 601 Solvent Atoms 14 Heterogen Atoms 23
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing