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Crystal Structure of Taniborbactam in complex with SME-1 class A Carbapenemase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M lithium chloride, PEG 4000 20%
Crystal Properties Matthews coefficient Solvent content 2.13 42.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.817 α = 90 b = 51.512 β = 113.075 c = 74.697 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU HyPix-6000HE 2024-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.8 24.887 99.9 0.961 11.8 6.1 46191
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 1.8 1.84 0.717
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 FREE R-VALUE 1.93 24.887 37522 1855 99.88 0.187 0.1842 0.1845 0.2384 0.2391 14.01
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] 0.659 -0.373 0.405 -0.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.447 r_dihedral_angle_3_deg 16.124 r_dihedral_angle_6_deg 14.968 r_dihedral_angle_1_deg 6.642 r_lrange_it 4.862 r_scangle_it 3.399 r_scbond_it 2.178 r_angle_refined_deg 1.948 r_mcangle_it 1.764 r_mcbond_it 1.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.447 r_dihedral_angle_3_deg 16.124 r_dihedral_angle_6_deg 14.968 r_dihedral_angle_1_deg 6.642 r_lrange_it 4.862 r_scangle_it 3.399 r_scbond_it 2.178 r_angle_refined_deg 1.948 r_mcangle_it 1.764 r_mcbond_it 1.098 r_nbtor_refined 0.31 r_symmetry_xyhbond_nbd_refined 0.24 r_symmetry_nbd_refined 0.234 r_nbd_refined 0.211 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.132 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing