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Long Interspersed Nuclear Element 1 (LINE-1) reverse transcriptase ternary complex with hybrid duplex and dTTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-O00370-F1 Truncated to residues 238-1061
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide 6 VAPOR DIFFUSION 5.6 293 PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide 5 VAPOR DIFFUSION 5.6 293 PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide 4 VAPOR DIFFUSION 5.6 293 PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide 3 VAPOR DIFFUSION 5.6 293 PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide 2 VAPOR DIFFUSION 5.6 293 PEG8000, sodium citrate, 1,4 dioxane, ethylene glycol, dimethyl sulphoxide
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.349 α = 90 b = 84.528 β = 91.48 c = 107.938 γ = 90
Symmetry Space Group C 1 2 1
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 XE 16M 2022-08-05 M SINGLE WAVELENGTH 6 6 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-08-06 M SINGLE WAVELENGTH 5 5 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-08-06 M SINGLE WAVELENGTH 4 4 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-08-06 M SINGLE WAVELENGTH 3 3 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-08-06 M SINGLE WAVELENGTH 2 2 x-ray 100 PIXEL DECTRIS EIGER2 XE 16M 2022-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03 6 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03 5 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03 4 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03 3 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1,2,3,4,5,6 2.1 59.66 100 0.018 1 18.7 41.2 62734 62715 49.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2,3,4,5,6 2.1 2.15 100 0.427 0.892 1.9 42.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.1 59.66 62715 3001 100 0.2093 0.2079 0.2023 0.238 0.2303 RANDOM 61.79
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] -22.1967 -9.7979 6.9248 15.2719
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.16 t_omega_torsion 3.1 t_angle_deg 0.89 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5573 Nucleic Acid Atoms 439 Solvent Atoms 219 Heterogen Atoms 128
Software Software Software Name Purpose BUSTER refinement DIALS data reduction Aimless data scaling PHASER phasing