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Crystal Structure of TgoT_PGLVVWA XNA Polymerase (Apo)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10 283 2 M ammonium sulfate, 0.1 M CAPS, 0.2 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.78 55.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.199 α = 90 b = 105.801 β = 90 c = 156.712 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 16M 2023-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.953738 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.18 56.2 100 0.0919 0.9977 12.09 8.78 53068
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 2.18 2.22 99.73 0.3317
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 2.18 52.9 1.33 52705 2639 99.3 0.231 0.2283 0.2285 0.2824 0.2824
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 6.867 f_angle_d 1.099 f_chiral_restr 0.06 f_plane_restr 0.016 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6227 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement DIALS data reduction DIALS data scaling MOLREP phasing