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KOD-H4 DNA polymerase mutant in a binary complex with DNA:DNA containing one HNA nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 12.5 % (w/v) PEG 4K, 20 % (v/v) 1,2,6-hexanetriol, 0.02 M DL-arginine-HCl- 0.02 M DL-threonine, 0.02 M D-sorbitol, 0.02 DL-histidine-HCl*H2O, 0.02 M DL-5-hydroxylysine-HCl, 0.02 M trans-4-hydroxy-L-proline, 0.1 M MOPSO/bis-tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.78 55.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.091 α = 90 b = 148.602 β = 90 c = 66.639 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 2023-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000020 SLS X06SA
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 2.7 49.534 99.9 0.991 3.66 4.35 58227
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 2.7 2.87 99.9 0.106
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 3 45.3 1.28 42334 2709 99.7 0.236 0.2337 0.234 0.27 0.2707 93.03
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 18.2255 f_angle_d 0.5448 f_chiral_restr 0.04 f_plane_restr 0.0045 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6200 Nucleic Acid Atoms 571 Solvent Atoms 9 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing