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Crystal structure of KPC-2 complexed with compound 22
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 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.411 α = 90 b = 59.778 β = 90 c = 78.317 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 PILATUS3 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 1.78 50 99.9 0.086 24.19 7.7 25968
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 1.78 1.81 0.384 3.77
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 1.78 45.82 24653 1280 99.82 0.15551 0.15364 0.1654 0.19142 0.2002 RANDOM 24.185
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] -1.78 -0.02 1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.503 r_dihedral_angle_4_deg 18.078 r_dihedral_angle_3_deg 12.414 r_long_range_B_refined 7.153 r_long_range_B_other 7.007 r_dihedral_angle_1_deg 6.613 r_scangle_other 5.742 r_scbond_it 4.404 r_scbond_other 4.156 r_mcangle_it 3.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.503 r_dihedral_angle_4_deg 18.078 r_dihedral_angle_3_deg 12.414 r_long_range_B_refined 7.153 r_long_range_B_other 7.007 r_dihedral_angle_1_deg 6.613 r_scangle_other 5.742 r_scbond_it 4.404 r_scbond_other 4.156 r_mcangle_it 3.585 r_mcangle_other 3.585 r_mcbond_it 2.732 r_mcbond_other 2.713 r_angle_refined_deg 1.733 r_angle_other_deg 1.496 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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 180 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing