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Crystal Structure of SME-1 Class A Carbapenemase in complex with Durlobactam
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 6.5 293 20% PEG 3350, 0.2M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 1.98 37.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.355 α = 90 b = 50.746 β = 92.705 c = 129.9 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 2024-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 25.95 99.9 0.166 0.994 7.5 7.5 20681
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 2.38 0.938
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 2.3 25.386 20666 1028 99.802 0.196 0.1926 0.1922 0.2682 0.2717 14.082
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] 2.603 -0.517 -1.689 -0.862
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.462 r_dihedral_angle_3_deg 18.598 r_dihedral_angle_6_deg 15.25 r_dihedral_angle_2_deg 11.235 r_dihedral_angle_1_deg 9.038 r_scangle_it 7.351 r_mcangle_it 5.886 r_rigid_bond_restr 5.476 r_scbond_it 4.974 r_mcbond_it 3.731
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 29.462 r_dihedral_angle_3_deg 18.598 r_dihedral_angle_6_deg 15.25 r_dihedral_angle_2_deg 11.235 r_dihedral_angle_1_deg 9.038 r_scangle_it 7.351 r_mcangle_it 5.886 r_rigid_bond_restr 5.476 r_scbond_it 4.974 r_mcbond_it 3.731 r_angle_refined_deg 2.397 r_symmetry_nbd_refined 0.344 r_nbtor_refined 0.313 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.227 r_symmetry_xyhbond_nbd_refined 0.177 r_chiral_restr 0.149 r_ncsr_local_group_1 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling MOLREP phasing