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Crystal structure of MnmM from S. aureus complexed with SAH (1.50 A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q2FXG9-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M BIS-TRIS pH 6.5 and 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.329 α = 91.25 b = 69.362 β = 112.97 c = 74.608 γ = 114.05
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 2022-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97949 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 1.5 67.09 92.7 0.069 0.074 0.028 0.999 14.7 7.3 104221 21.6
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 1.5 1.68 72.3 1.285 1.382 0.507 0.637 1.7 7.4
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) 1.5 67.09 98695 5112 63.35 0.18451 0.18281 0.1899 0.21855 0.2247 RANDOM 30.373
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] 0.06 0.04 0.02 0.51 0.01 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 16.372 r_dihedral_angle_3_deg 12.909 r_long_range_B_refined 7.05 r_long_range_B_other 7.013 r_dihedral_angle_1_deg 6.641 r_scangle_other 4.481 r_mcangle_other 3.15 r_mcangle_it 3.149 r_scbond_it 2.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.242 r_dihedral_angle_4_deg 16.372 r_dihedral_angle_3_deg 12.909 r_long_range_B_refined 7.05 r_long_range_B_other 7.013 r_dihedral_angle_1_deg 6.641 r_scangle_other 4.481 r_mcangle_other 3.15 r_mcangle_it 3.149 r_scbond_it 2.942 r_scbond_other 2.942 r_mcbond_it 2.132 r_mcbond_other 2.13 r_angle_refined_deg 1.652 r_angle_other_deg 1.207 r_chiral_restr 0.118 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8298 Nucleic Acid Atoms Solvent Atoms 678 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement MxDC data collection XDS data reduction STARANISO data scaling Coot model building MOLREP phasing PDB_EXTRACT data extraction