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Crystal structure of KPC-2 complexed with compound 21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 2.0 M Ammonium sulfate, 5% ethanol
Crystal Properties Matthews coefficient Solvent content 2.1 41.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.166 α = 90 b = 59.968 β = 90 c = 76.932 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.978 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.98 50 99.6 0.1 21.82 7.7 18153
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.01 0.438 3.8
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 (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 1.99 45.36 17257 863 99 0.16489 0.16291 0.1725 0.20467 0.2148 RANDOM 29.987
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] -0.03 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.558 r_dihedral_angle_4_deg 15.745 r_dihedral_angle_3_deg 14.531 r_long_range_B_refined 7.762 r_long_range_B_other 7.761 r_dihedral_angle_1_deg 6.942 r_scangle_other 4.5 r_scbond_it 3.243 r_mcangle_it 3.117 r_mcangle_other 3.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.558 r_dihedral_angle_4_deg 15.745 r_dihedral_angle_3_deg 14.531 r_long_range_B_refined 7.762 r_long_range_B_other 7.761 r_dihedral_angle_1_deg 6.942 r_scangle_other 4.5 r_scbond_it 3.243 r_mcangle_it 3.117 r_mcangle_other 3.116 r_scbond_other 3.089 r_mcbond_it 2.231 r_mcbond_other 2.222 r_angle_refined_deg 1.506 r_angle_other_deg 1.377 r_chiral_restr 0.074 r_bond_refined_d 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2013 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing