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Crystal structure KPC-2 beta-lactamase complexed with WCK 5153 by co-crystallization
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 200mM Lithium sulfate, 100mM sodium acetate pH 4.4-4.6, and 28-31% PEG8000. Protein to inhibitor molar ratio of 1 is to 10 and KPC-2 concentration was 10 mg/mL
Crystal Properties Matthews coefficient Solvent content 1.86 33.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.529 α = 87.66 b = 37.349 β = 89.71 c = 82.07 γ = 84.31
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.12708 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 37.13 95.5 0.046 0.065 0.046 0.997 14 2 35965
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 92 0.272 0.384 0.272 0.8 2
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 1.8 37.13 34166 1799 95.49 0.151 0.1486 0.1593 0.1966 0.2028 RANDOM 14.148
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 0.01 -0.01 -0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.202 r_dihedral_angle_4_deg 16.043 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_1_deg 6.369 r_angle_refined_deg 1.694 r_angle_other_deg 1.097 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.202 r_dihedral_angle_4_deg 16.043 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_1_deg 6.369 r_angle_refined_deg 1.694 r_angle_other_deg 1.097 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3975 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 77
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction