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Crystal structure of MnmM from S. aureus complexed with SAM and tRNA anti-codon stem loop (ASL) (1.55 A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold model (UniProt: Q2FXG9)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.5, 20% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.47 50.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.436 α = 90 b = 71.494 β = 111.6 c = 67.267 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 100 PIXEL DECTRIS EIGER X 9M 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0000 PAL/PLS 5C (4A)
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 1.55 47.12 84.6 0.088 0.095 0.035 0.998 11.8 7.2 65003
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 1.55 1.66 29.6 1.421 1.531 0.566 0.537 1.4 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT AlphaFold model (UniProt: Q2FXG9) 1.55 47.12 61827 3175 84.55 0.1758 0.17432 0.1845 0.20433 0.2143 RANDOM 29.176
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] -0.18 -0.11 -0.04 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 17.453 r_dihedral_angle_3_deg 12.963 r_dihedral_angle_1_deg 6.251 r_long_range_B_refined 5.421 r_long_range_B_other 5.25 r_scangle_other 2.006 r_angle_refined_deg 1.52 r_mcangle_it 1.425 r_mcangle_other 1.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 17.453 r_dihedral_angle_3_deg 12.963 r_dihedral_angle_1_deg 6.251 r_long_range_B_refined 5.421 r_long_range_B_other 5.25 r_scangle_other 2.006 r_angle_refined_deg 1.52 r_mcangle_it 1.425 r_mcangle_other 1.424 r_scbond_it 1.295 r_scbond_other 1.295 r_angle_other_deg 1.235 r_mcbond_it 0.907 r_mcbond_other 0.905 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3028 Nucleic Acid Atoms 710 Solvent Atoms 421 Heterogen Atoms 55
Software Software Software Name Purpose MxDC data collection XDS data reduction STARANISO data scaling MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction