☰ Navigation Tabs
Crystal structure of LINE-1 ribozyme mutant - C39U
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other RNAComposer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.01 M Magnesium Chloride
0.05 M MES pH 5.6
2.0 M Lithium Sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 6.41 80.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.871 α = 90 b = 94.871 β = 90 c = 261.635 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 EIGER2 X 4M 2021-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979137 SSRF BL02U1
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 2.71 50 99.8 0.992 5.8 5.2 19754
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 2.72 2.87 0.464
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 2.71 44.59 1.33 19571 955 99.18 0.2203 0.219 0.22 0.2463 0.2456
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 12.039 f_angle_d 0.915 f_chiral_restr 0.044 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 20 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction DIALS data scaling PHASER phasing