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Crystal structure of MnmM from S. aureus in apo state (1.44 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 sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.68 54.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.494 α = 90 b = 63.91 β = 90 c = 135.044 γ = 90
Symmetry Space Group P 21 21 21
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) 0.97965 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 1.44 47.34 95.5 0.073 0.076 0.021 0.999 17.1 13.3 67371 20.9
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 1.44 1.54 66.5 1.955 2.025 0.525 0.605 1.5 14.8
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) 1.44 47.34 63959 3409 84.1 0.15394 0.15185 0.161 0.19218 0.1981 RANDOM 26.467
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] -1.05 -0.29 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 15.031 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_1_deg 6.467 r_long_range_B_refined 4.411 r_long_range_B_other 4.021 r_scangle_other 3.322 r_mcangle_it 2.835 r_mcangle_other 2.826 r_scbond_it 2.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.636 r_dihedral_angle_4_deg 15.031 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_1_deg 6.467 r_long_range_B_refined 4.411 r_long_range_B_other 4.021 r_scangle_other 3.322 r_mcangle_it 2.835 r_mcangle_other 2.826 r_scbond_it 2.679 r_scbond_other 2.678 r_rigid_bond_restr 2.432 r_mcbond_it 2.094 r_mcbond_other 2.084 r_angle_refined_deg 1.482 r_angle_other_deg 1.235 r_chiral_restr 0.114 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2860 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms
Software Software Software Name Purpose MxDC data collection STARANISO data scaling XDS data reduction MOLREP phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction