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Crystal structure of the alkyltransferase ribozyme SAMURI co-crystalized 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 2.71 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.444 α = 90 b = 75.444 β = 90 c = 72.251 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 EIGER2 X 16M 2023-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 0.979 PETRA III, DESY P11
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 42.92 99.9 0.06 0.065 0.02 0.999 22.1 14 18088 126.4
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 2.112 2.27 0.593 0.591 1.2 14.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.9 42.92 0.91 16289 725 92.53 0.2015 0.2005 0.2114 0.224 0.2372 4.45% random 52.85
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 24.0165 f_angle_d 0.5521 f_chiral_restr 0.0273 f_bond_d 0.0018 f_plane_restr 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2498 Solvent Atoms 33 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction AutoSol phasing Coot model building