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Crystal structure of MnmM from B. subtilis complexed with Gln-TTG anti-codon stem loop and SAM (2.90 A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PON PDB entry 4PON
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M Ammonium acetate,
0.1 M Sodium citrate tribasic dehydrate pH5.6,
30% w/v Polyethylene glycol 4,000,
3% w/v Trimethylamine N-oxide dihydrate
Crystal Properties Matthews coefficient Solvent content 2.43 49.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.18 α = 90.97 b = 60.755 β = 93.1 c = 94.059 γ = 101.55
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 2.9 93.88 91.2 0.165 0.195 0.102 0.992 6.6 3.5 18875
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 2.9 3.08 97.5 0.995 1.169 0.607 0.768 1.2 3.6
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 PDB entry 4PON 2.9 93.88 17930 901 90.98 0.24281 0.24076 0.2531 0.2852 0.2975 RANDOM 72.123
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] 4.78 0.84 7.38 -8.95 1.66 3.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.538 r_long_range_B_refined 13.789 r_long_range_B_other 13.788 r_mcangle_it 10.157 r_mcangle_other 10.156 r_scangle_other 9.356 r_dihedral_angle_2_deg 8.287 r_dihedral_angle_1_deg 7.61 r_mcbond_it 6.268 r_mcbond_other 6.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.538 r_long_range_B_refined 13.789 r_long_range_B_other 13.788 r_mcangle_it 10.157 r_mcangle_other 10.156 r_scangle_other 9.356 r_dihedral_angle_2_deg 8.287 r_dihedral_angle_1_deg 7.61 r_mcbond_it 6.268 r_mcbond_other 6.265 r_scbond_it 5.763 r_scbond_other 5.76 r_angle_refined_deg 1.263 r_angle_other_deg 0.407 r_chiral_restr 0.056 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5423 Nucleic Acid Atoms 710 Solvent Atoms 110 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing MxDC data collection PDB_EXTRACT data extraction Coot model building