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Atomic Resolution X-Ray Crystal Structure of a Ruthenocene Conjugated Beta-Lactam Antibiotic in Complex with CTX-M-14 S70G Beta-Lactamase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XXR PDB entry 4XXR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 293.15 potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.093 α = 90 b = 106.821 β = 101.66 c = 47.933 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX300-HS 2015-04-01 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 1.18 50 97.7 0.036 25.8 3.7 133593
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 1.18 1.2 88.6 4.3 3.1
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 4XXR 1.18 50 133593 7118 96.77 0.12848 0.12756 0.1279 0.14633 0.146 RANDOM 16.345
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] 0.44 -0.55 -0.47 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.426 r_sphericity_free 25.087 r_dihedral_angle_4_deg 14.804 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.983 r_sphericity_bonded 6.604 r_rigid_bond_restr 3.378 r_long_range_B_refined 1.76 r_long_range_B_other 1.76 r_angle_refined_deg 1.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.426 r_sphericity_free 25.087 r_dihedral_angle_4_deg 14.804 r_dihedral_angle_3_deg 14.342 r_dihedral_angle_1_deg 6.983 r_sphericity_bonded 6.604 r_rigid_bond_restr 3.378 r_long_range_B_refined 1.76 r_long_range_B_other 1.76 r_angle_refined_deg 1.345 r_angle_other_deg 0.687 r_mcangle_it 0.645 r_mcangle_other 0.645 r_scangle_other 0.613 r_mcbond_it 0.445 r_mcbond_other 0.445 r_scbond_it 0.44 r_scbond_other 0.44 r_chiral_restr 0.085 r_gen_planes_refined 0.011 r_bond_refined_d 0.007 r_gen_planes_other 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3903 Nucleic Acid Atoms Solvent Atoms 578 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing