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KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing two AtNA nucleotides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02 M sodium formate, 0.02 M ammonium acetate,
0.02 M trisodium citrate, 0.02 M sodium potassium
l-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.472 α = 90 b = 153.471 β = 90 c = 69.03 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) 0.976260 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 2.6 43.37 99.82 0.99 6.52 6 70222 64.31
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 2.6 2.66 0.784 1.3
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 2.6 43.37 1.11 70179 2088 99.82 0.2005 0.1988 0.1988 0.2586 0.2582 73.89
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 22.0238 f_angle_d 0.5463 f_chiral_restr 0.0409 f_plane_restr 0.0047 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6200 Nucleic Acid Atoms 591 Solvent Atoms 140 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing