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TNA polymerase, 7-47, 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, 19 % glycerol, and 9 % polyethylene glycol 4000
Crystal Properties Matthews coefficient Solvent content 3.01 59.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.216 α = 90 b = 110.57 β = 90 c = 124.26 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 16M 2023-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1 SSRL BL12-2
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 50.6 98.23 0.07 0.99 10.94 3.4 62311 23.69
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 2.18 2.258 0.265 0.772
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 50.6 1.34 62311 2000 98.24 0.1896 0.1884 0.189 0.2258 0.2257 27.13
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 16.58 f_angle_d 1.0012 f_chiral_restr 0.0407 f_plane_restr 0.0038 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6238 Nucleic Acid Atoms 635 Solvent Atoms 440 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection iMOSFLM data reduction pointless data scaling Aimless data scaling PHASER phasing Coot model building