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Crystal Structure of SME-1 Carbapenemase in complex with Nacubactam.
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, 0.2 M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 2.26 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.731 α = 90 b = 52.206 β = 114.549 c = 78.133 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 2024-06-12 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) R Merge I (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 2.07 24.65 99.9 0.096 0.995 14.6 6.5 32338
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 2.07 2.13 0.821
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 2.07 24.65 32325 1640 99.907 0.181 0.1775 0.1778 0.2353 0.2356 18.505
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] -1.154 -0.354 0.583 0.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.382 r_dihedral_angle_6_deg 14.512 r_lrange_it 9.547 r_dihedral_angle_2_deg 7.543 r_dihedral_angle_1_deg 6.612 r_scangle_it 3.377 r_rigid_bond_restr 2.722 r_mcangle_it 2.453 r_scbond_it 2.205 r_angle_refined_deg 1.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.382 r_dihedral_angle_6_deg 14.512 r_lrange_it 9.547 r_dihedral_angle_2_deg 7.543 r_dihedral_angle_1_deg 6.612 r_scangle_it 3.377 r_rigid_bond_restr 2.722 r_mcangle_it 2.453 r_scbond_it 2.205 r_angle_refined_deg 1.813 r_mcbond_it 1.482 r_nbtor_refined 0.302 r_symmetry_nbd_refined 0.284 r_symmetry_xyhbond_nbd_refined 0.222 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.121 r_ncsr_local_group_1 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4130 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling MOLREP phasing