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CRYSTAL STRUCTURE OF THE KPC-2 D179N VARIANT IN COMPLEX WITH RELEBACTAM (IMINE HYDROLYSIS INTERMEDIATE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 100 mM HEPES pH 8.0 and 0.8 M NaH2PO4, 0.8 M KH2PO4
Crystal Properties Matthews coefficient Solvent content 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.795 α = 90 b = 66.227 β = 90 c = 72.977 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 EIGER X 16M 2020-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97935 NSLS-II 17-ID-2
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 1.26 29.63 99.9 0.068 1 21 13.1 66874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.29 98.4 0.683 0.931 3.5 12.5
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 (Observed) 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 2OV5 1.26 27.76 63495 3309 99.87 0.13538 0.13372 0.1338 0.16746 0.1673 RANDOM 14.705
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] -0.02 0.07 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.109 r_dihedral_angle_4_deg 15.743 r_dihedral_angle_3_deg 12.201 r_mcangle_it 6.883 r_mcangle_other 6.882 r_dihedral_angle_1_deg 6.593 r_long_range_B_refined 6.231 r_long_range_B_other 6.012 r_rigid_bond_restr 4.975 r_mcbond_other 4.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.109 r_dihedral_angle_4_deg 15.743 r_dihedral_angle_3_deg 12.201 r_mcangle_it 6.883 r_mcangle_other 6.882 r_dihedral_angle_1_deg 6.593 r_long_range_B_refined 6.231 r_long_range_B_other 6.012 r_rigid_bond_restr 4.975 r_mcbond_other 4.631 r_mcbond_it 4.628 r_scangle_other 3.089 r_scbond_other 2.546 r_scbond_it 2.544 r_angle_other_deg 1.513 r_angle_refined_deg 1.502 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1965 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 24
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction PHASER phasing