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NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP57
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TGD 6TGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M HEPES, 0.1 M MOPS, pH 7.5, 0.03 M MgCl2 hexahydrate, 0.03 M CaCl2 dihydrate, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.95 37.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.068 α = 90 b = 70.444 β = 90 c = 73.803 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 EIGER2 XE 16M 2022-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.873 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.78 53.31 100 0.178 6.8 7.1 39230
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.82 100 0.956 2.1 7
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 (All) 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 6TGD 1.78 53.306 39169 1900 99.931 0.185 0.184 0.1853 0.2073 0.208 RANDOM 26
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] 0.603 1.418 -2.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.708 r_dihedral_angle_4_deg 21.34 r_dihedral_angle_3_deg 13.673 r_dihedral_angle_1_deg 6.777 r_lrange_it 6.145 r_scangle_it 4.862 r_scbond_it 3.278 r_mcangle_it 3.065 r_mcbond_it 2.182 r_angle_refined_deg 1.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.708 r_dihedral_angle_4_deg 21.34 r_dihedral_angle_3_deg 13.673 r_dihedral_angle_1_deg 6.777 r_lrange_it 6.145 r_scangle_it 4.862 r_scbond_it 3.278 r_mcangle_it 3.065 r_mcbond_it 2.182 r_angle_refined_deg 1.574 r_symmetry_nbd_refined 0.328 r_nbtor_refined 0.318 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.197 r_xyhbond_nbd_refined 0.126 r_metal_ion_refined 0.114 r_chiral_restr 0.105 r_gen_planes_refined 0.01 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3434 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing