☰ Navigation Tabs
Crystal structure of the methyltransferase ribozyme 1 with two 2'O-methylation (MTR1m2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Q7X search for 1 copy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293.15 200 uM RNA in a ratio of A:B:C=1:1:1 in 10 mM HEPES pH7.5, 50 mM potassium chloride, 5 mM magnesium chloride and 240 uM of O6-methylguanine
Crystallization cocktail:
100 mM NaCl, 100 mM LiCl, 10 mM MgCl2, 50 mM MES pH 6.4-6.7, 36-42% MPD
Crystal Properties Matthews coefficient Solvent content 2.53 67.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.323 α = 90 b = 71.323 β = 90 c = 83.512 γ = 90
Symmetry Space Group P 41 21 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 16M 2021-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 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 2.6 43.17 100 0.044 0.045 0.01 1 42.9 25.3 7084 3 76.8
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 2.6 2.72 100 2.017 2.039 0.396 0.583 2 27
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 2.6 43.17 1.37 7047 347 99.96 0.2216 0.2201 0.2186 0.251 0.2496 44.34
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 24.5219 f_angle_d 0.9398 f_chiral_restr 0.0357 f_bond_d 0.0053 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1314 Solvent Atoms 45 Heterogen Atoms 15
Software Software Software Name Purpose XDS data reduction PHASER phasing Coot model building PHENIX refinement XDS data scaling