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the wildtype SAM-VI riboswitch bound to a N-mustard SAM analog M1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M sodium acetate trihydrate pH 4.6, 10% w/v polyethylene glycol 4,000
Crystal Properties Matthews coefficient Solvent content 3.17 61.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.39 α = 90 b = 85.348 β = 105.46 c = 93.165 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2019-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.102 SSRF BL17U1
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 2.76 42.67 94.8 0.075 0.081 0.031 0.998 15.9 6.9 20968 73.11
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 2.76 2.9 95.4 0.704 0.761 0.285 0.885 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6LAS 2.76 42.67 1.39 20945 984 94.6 0.1897 0.188 0.1898 0.2234 0.2214 79.1927
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 19.739 f_angle_d 1.181 f_chiral_restr 0.062 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2173 Nucleic Acid Atoms 2368 Solvent Atoms 18 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction XDS data scaling PHASER phasing