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Crystal structure of KPC-2 beta-lactamase complexed with avibactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RXW PDB entry 3RXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 20% PEG6000, 100 mM potassium thiocyanate, 100 mM citrate, pH 4.0, crystals soaked for 8 minutes with 5 mM avibactam in mother liquor (25% PEG600, 100 mM citrate, pH 5.0)
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.315 α = 90 b = 66.695 β = 90 c = 73.208 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 CCD ADSC QUANTUM 315r 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.1272 SSRL BL7-1
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 1.8 50 93.2 0.053 15.7 2.9 22206
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 1.8 1.86 88.2 0.444 1.9 2.6
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 PDB entry 3RXW 1.8 36.6 21017 1136 92.83 0.15569 0.15247 0.1667 0.21912 0.2209 RANDOM 24.22
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.76 r_dihedral_angle_4_deg 18.62 r_dihedral_angle_3_deg 14.157 r_long_range_B_refined 7.718 r_long_range_B_other 7.514 r_dihedral_angle_1_deg 6.392 r_scangle_other 6.172 r_scbond_it 4.604 r_scbond_other 4.603 r_mcangle_it 3.442
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.76 r_dihedral_angle_4_deg 18.62 r_dihedral_angle_3_deg 14.157 r_long_range_B_refined 7.718 r_long_range_B_other 7.514 r_dihedral_angle_1_deg 6.392 r_scangle_other 6.172 r_scbond_it 4.604 r_scbond_other 4.603 r_mcangle_it 3.442 r_mcangle_other 3.433 r_mcbond_it 2.998 r_mcbond_other 2.986 r_angle_refined_deg 1.77 r_angle_other_deg 0.926 r_chiral_restr 0.224 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 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 1972 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing