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NDM-1 metallo-beta-lactamase in complex with triazole-based inhibitor CP56
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 1.91 35.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.61 α = 90 b = 73.964 β = 90 c = 77.115 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 1.6 34.19 100 0.161 6.8 6.6 52482
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 1.6 1.63 100 0.92 2.1 6.3
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 1.6 34.19 52418 2595 99.907 0.175 0.1731 0.1737 0.209 0.2085 Random 23
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] 0.969 -1.124 0.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.793 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_1_deg 6.506 r_lrange_it 5.551 r_scangle_it 4.612 r_scbond_it 3.168 r_mcangle_it 2.941 r_mcbond_it 2.01 r_angle_refined_deg 1.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.793 r_dihedral_angle_4_deg 21.084 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_1_deg 6.506 r_lrange_it 5.551 r_scangle_it 4.612 r_scbond_it 3.168 r_mcangle_it 2.941 r_mcbond_it 2.01 r_angle_refined_deg 1.642 r_nbtor_refined 0.32 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.155 r_chiral_restr 0.104 r_xyhbond_nbd_refined 0.104 r_metal_ion_refined 0.098 r_gen_planes_refined 0.01 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3425 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing