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Crystal structure of D179N KPC-2 beta-lactamase in complex with vaborbactam
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 4 298 0.1 M Sodium citrate HCl pH 4, 0.8 M Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.19 43.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.209 α = 90 b = 66.021 β = 90 c = 72.95 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 EIGER2 S 16M 2020-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97935 NSLS-II 17-ID-1
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 1.16 27.76 98.8 0.064 1 20.2 12.6 83367
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 1.16 1.2 84.2 0.62 0.88 2.6 8.9
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 1.16 27.76 80550 4171 98.56 0.1289 0.1274 0.1274 0.1576 0.1571 RANDOM 12.372
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] -0.01 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.478 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 11.358 r_dihedral_angle_1_deg 6.47 r_rigid_bond_restr 4.315 r_angle_refined_deg 2.002 r_angle_other_deg 1.7 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.478 r_dihedral_angle_4_deg 17.371 r_dihedral_angle_3_deg 11.358 r_dihedral_angle_1_deg 6.47 r_rigid_bond_restr 4.315 r_angle_refined_deg 2.002 r_angle_other_deg 1.7 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1977 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 30
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XDS data scaling PHASER phasing