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Crystal structure of metformin hydrolase (MfmAB) from Pseudomonas mendocina sp. MET-2 apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A2S0XPN7 used for modelling MfmA in silico model AlphaFold A0A316GGX0 used for modelling MfmB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 1 uL 10 mg/mL protein + 1 uL 13.5% w/v PEG3350, 0.1 M Bis-Tris propane, 0.2 M NaNO3, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.53 α = 93.429 b = 107.88 β = 97.625 c = 114.51 γ = 98.105
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 16M 2022-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 80 91.2 0.999 12.75 2.0558 224389
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 89 0.745 1.59
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.2 74.608 224388 11220 91.205 0.215 0.2125 0.2178 0.257 0.2593 50.927
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] 0.408 -0.565 -0.543 0.2 0.612 -0.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.624 r_dihedral_angle_6_deg 15.9 r_dihedral_angle_2_deg 7.954 r_lrange_it 7.761 r_lrange_other 7.752 r_dihedral_angle_1_deg 7.219 r_scangle_it 4.558 r_scangle_other 4.558 r_mcangle_it 4.253 r_mcangle_other 4.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.624 r_dihedral_angle_6_deg 15.9 r_dihedral_angle_2_deg 7.954 r_lrange_it 7.761 r_lrange_other 7.752 r_dihedral_angle_1_deg 7.219 r_scangle_it 4.558 r_scangle_other 4.558 r_mcangle_it 4.253 r_mcangle_other 4.253 r_scbond_it 2.878 r_scbond_other 2.878 r_mcbond_it 2.77 r_mcbond_other 2.77 r_angle_refined_deg 1.314 r_angle_other_deg 0.457 r_nbd_other 0.22 r_nbd_refined 0.217 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.181 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31104 Nucleic Acid Atoms Solvent Atoms 910 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building