☰ Navigation Tabs
Crystal structure of KOD DNA Polymerase in a binary complex with Hypoxanthine containing template
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 7.5 291.15 Morpheus E7: 0.12 M ethylene glycols (0.3 M diethylene glycol, 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol), 0.1 M sodium HEPES/MOPS pH 7.5, 50 % (v/v) of a mixture of glycerol (40 % v/v) and PEG 4000 (20 % w/v).
Crystal Properties Matthews coefficient Solvent content 2.66 53.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.356 α = 90 b = 142.936 β = 90 c = 65.582 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 2019-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000089622351307 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.91 48.32 93.3 0.148 0.996 7.39 4.6 147921 35.88
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 1.91 2.03 64.8 0.185 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4K8Z 1.92 44.45 1.33 144954 3691 92.38 0.1841 0.1829 0.1827 0.2337 0.2333 46
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 18.2237 f_angle_d 1.214 f_chiral_restr 0.0614 f_bond_d 0.0123 f_plane_restr 0.0118
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6239 Nucleic Acid Atoms 667 Solvent Atoms 382 Heterogen Atoms 27
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing