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Crystal structure of the alkyltransferase ribozyme SAMURI co-crystallized with SAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FN3 Crystal structure of SAMURI with ProSeDMA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 50 mM MES pH6.5
100 mM NaCl
100 mM LiCl
15 mM MgCl2
39% MPD
Crystal Properties Matthews coefficient Solvent content 2.64 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.444 α = 90 b = 75.444 β = 90 c = 73.15 γ = 90
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 2023-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.9 43.1 99.9 0.051 0.052 0.015 1 24.9 13.9 9208 113
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 100 1.18 1.223 0.326 0.833 2.4 14
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 2.9 33.74 1.36 9188 489 99.9 0.2056 0.2042 0.2091 0.2303 0.2356 52.09
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 17.1532 f_angle_d 0.5563 f_chiral_restr 0.026 f_plane_restr 0.0021 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2494 Solvent Atoms 40 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building