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Crystal structure of CTX-M-15 extended-spectrum beta-lactamase in complex with avibactam (NXL104)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HBT PDB ENTRY 4HBT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris-HCl, 2.2-2.4M ammonium sulfate, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.483 α = 90 b = 45.686 β = 90 c = 117.721 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 MARMOSAIC 225 mm CCD 2009-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.918 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 23.54 99.9 98124 98124 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4HBT 1.1 22.84 98145 93132 4899 99.87 0.1169 0.10531 0.10441 0.12241 0.1348 RANDOM 7.278
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 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.447 r_sphericity_free 30.87 r_dihedral_angle_3_deg 10.837 r_dihedral_angle_4_deg 10.794 r_sphericity_bonded 9.169 r_rigid_bond_restr 8.015 r_dihedral_angle_1_deg 5.983 r_angle_refined_deg 2.625 r_angle_other_deg 1.27 r_chiral_restr 0.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.447 r_sphericity_free 30.87 r_dihedral_angle_3_deg 10.837 r_dihedral_angle_4_deg 10.794 r_sphericity_bonded 9.169 r_rigid_bond_restr 8.015 r_dihedral_angle_1_deg 5.983 r_angle_refined_deg 2.625 r_angle_other_deg 1.27 r_chiral_restr 0.415 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1953 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 78
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling