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Crystal structure of KPC-2 complexed with compound 14
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 2.15 42.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.382 α = 90 b = 59.73 β = 90 c = 78.699 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 EIGER2 S 16M 2022-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-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 1.57 50 98 0.087 25.16 7 37032
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 1.57 1.6 0.471 2.68
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 1.57 45.88 35232 1762 98.37 0.15704 0.15537 0.1676 0.18948 0.1961 RANDOM 19.771
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] -1.08 -0.76 1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.769 r_dihedral_angle_4_deg 16.091 r_dihedral_angle_3_deg 11.829 r_dihedral_angle_1_deg 6.775 r_long_range_B_refined 6.487 r_long_range_B_other 6.335 r_scangle_other 4.414 r_scbond_other 3.141 r_scbond_it 3.14 r_mcangle_other 2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.769 r_dihedral_angle_4_deg 16.091 r_dihedral_angle_3_deg 11.829 r_dihedral_angle_1_deg 6.775 r_long_range_B_refined 6.487 r_long_range_B_other 6.335 r_scangle_other 4.414 r_scbond_other 3.141 r_scbond_it 3.14 r_mcangle_other 2.68 r_mcangle_it 2.678 r_mcbond_it 1.803 r_mcbond_other 1.785 r_angle_refined_deg 1.72 r_angle_other_deg 1.559 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 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 246 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing