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Crystal structure of metformin hydrolase (MfmAB) from Pseudomonas mendocina sp. MET-2 with Ni2+2 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold A0A2S0XPN7 used for macromolecule metformin hydrolase subunit A in silico model AlphaFold A0A316GGX0 used for macromolecule metformin hydrolase subunit B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 1 uL 10 mg/mL protein + 1 uL 14.5% w/v PEG3350, 0.1 M Bis-Tris propane, 0.2 M NaNO3, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.4 α = 115.5 b = 96.4 β = 106.2 c = 96.7 γ = 101.1
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 PILATUS3 6M 2023-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
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 2.3 80 91.3 0.998 13.3 2.408 99100
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 2.3 2.4 88.6 0.96 3.07
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 2.3 19.865 99098 5056 91.623 0.174 0.1719 0.1705 0.2194 0.2116 76.693
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] -3.769 2.669 3.824 -2.678 2.882 -0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.418 r_dihedral_angle_6_deg 15.517 r_lrange_other 10.237 r_lrange_it 10.232 r_scangle_it 8.718 r_scangle_other 8.718 r_dihedral_angle_2_deg 8.088 r_dihedral_angle_1_deg 7.287 r_mcangle_it 6.472 r_mcangle_other 6.472
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.418 r_dihedral_angle_6_deg 15.517 r_lrange_other 10.237 r_lrange_it 10.232 r_scangle_it 8.718 r_scangle_other 8.718 r_dihedral_angle_2_deg 8.088 r_dihedral_angle_1_deg 7.287 r_mcangle_it 6.472 r_mcangle_other 6.472 r_scbond_it 6.167 r_scbond_other 6.167 r_mcbond_it 4.992 r_mcbond_other 4.992 r_angle_refined_deg 1.449 r_angle_other_deg 0.493 r_nbd_refined 0.221 r_symmetry_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.195 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.184 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.171 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.075 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15458 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building