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Crystal structure of MnmM from S. aureus complexed with SAM (2.04 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 lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 6.5, and 25% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 2.69 54.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.015 α = 90 b = 114.015 β = 90 c = 67.009 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 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 2.04 43.46 84.6 0.108 0.112 0.03 0.999 17.8 13.9 46406 40.76
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 2.04 2.23 36.4 2.271 2.353 0.615 0.627 1.4 14.6
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) 2.04 43.46 44157 2248 84.57 0.19058 0.18887 0.1972 0.22359 0.2301 RANDOM 53.712
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] -0.21 -0.21 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.711 r_dihedral_angle_4_deg 14.911 r_dihedral_angle_3_deg 14.357 r_long_range_B_refined 7.055 r_long_range_B_other 7.001 r_dihedral_angle_1_deg 6.189 r_scangle_other 4.772 r_mcangle_it 3.971 r_mcangle_other 3.971 r_scbond_it 3.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.711 r_dihedral_angle_4_deg 14.911 r_dihedral_angle_3_deg 14.357 r_long_range_B_refined 7.055 r_long_range_B_other 7.001 r_dihedral_angle_1_deg 6.189 r_scangle_other 4.772 r_mcangle_it 3.971 r_mcangle_other 3.971 r_scbond_it 3.181 r_scbond_other 3.181 r_mcbond_it 2.676 r_mcbond_other 2.675 r_angle_refined_deg 1.313 r_angle_other_deg 1.068 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5635 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MxDC data collection XDS data reduction STARANISO data scaling MOLREP phasing Coot model building PDB_EXTRACT data extraction