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Crystal Structure of SME-1 Carbapenemase in complex with Zidebactam
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 20% PEG 4000, 0.2M lithium chloride
Crystal Properties Matthews coefficient Solvent content 1.84 33.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.884 α = 90 b = 50.18 β = 97.939 c = 60.586 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 2024-06-19 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 2.4 23.159 99.9 0.997 15.9 8.3 8470
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 2.4 2.49 0.972
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 2.4 23.159 8453 418 99.764 0.187 0.1833 0.1826 0.2668 0.2666 20.373
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] -2.893 0.216 0.143 2.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.488 r_dihedral_angle_2_deg 14.165 r_dihedral_angle_6_deg 13.505 r_dihedral_angle_1_deg 6.881 r_lrange_it 6.588 r_rigid_bond_restr 3.428 r_scangle_it 2.542 r_mcangle_it 2.351 r_angle_refined_deg 1.927 r_scbond_it 1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.488 r_dihedral_angle_2_deg 14.165 r_dihedral_angle_6_deg 13.505 r_dihedral_angle_1_deg 6.881 r_lrange_it 6.588 r_rigid_bond_restr 3.428 r_scangle_it 2.542 r_mcangle_it 2.351 r_angle_refined_deg 1.927 r_scbond_it 1.57 r_mcbond_it 1.394 r_symmetry_xyhbond_nbd_refined 0.508 r_nbtor_refined 0.305 r_symmetry_nbd_refined 0.27 r_nbd_refined 0.222 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.126 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2058 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing