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Crystal structure of LINE-1 ribozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Z8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.02 M Calcium Chloride dihydrate
0.1 M Sodium Acetate trihydrate pH 4.6
30% v/v 2-Methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 6.22 80.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.247 α = 90 b = 93.247 β = 90 c = 262.655 γ = 120
Symmetry Space Group P 61 2 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 PILATUS3 6M 2021-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97853 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.86 80.75 98.2 0.999 22 18 6885
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 3.86 4.06 0.976
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 3.86 36.67 1.35 6768 337 97.61 0.3151 0.3136 0.3141 0.3457 0.3458
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 14.756 f_angle_d 1.005 f_chiral_restr 0.049 f_plane_restr 0.007 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1762 Solvent Atoms 4 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement xia2 data reduction xia2 data scaling PHASER phasing