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TNA polymerase, 10-92, binary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8T3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.06 M magnesium chloride hexahydrate, 0.06 M calcium chloride dihydrate, 0.1 M imidazole, 0.1 M 2-(N-morpholino) ethanesulfonic acid pH 6, 17.5 % glycerol, and 7.5 % polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 2.91 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.437 α = 90 b = 108.253 β = 90 c = 123.775 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 EIGER X 9M 2023-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X17B1 1 NSLS X17B1
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 2.17 33.3 99.79 0.1051 0.998 10.73 6.8 61779 51.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.172 2.25 2.163 0.365
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 2.17 33.3 1.34 61779 2000 99.83 0.2173 0.2163 0.2164 0.2471 0.2473 61
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 16.7619 f_angle_d 0.463 f_chiral_restr 0.0392 f_plane_restr 0.0039 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6243 Nucleic Acid Atoms 635 Solvent Atoms 84 Heterogen Atoms 4
Software Software Software Name Purpose XDS data reduction pointless data scaling Aimless data scaling PHASER phasing PHENIX refinement Coot model building