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Crystal structure of AmpC from Pseudomonas aeruginosa in complex with [3-(2-carboxyvinyl)phenyl]boronic acid] inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 294 1.8 M potassium phosphate buffer, pH 8.7
Crystal Properties Matthews coefficient Solvent content 2.81 56.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.678 α = 90 b = 82.678 β = 90 c = 123.563 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS3 6M 2016-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97779 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.78 46.78 97.8 0.042 0.999 12.6 3.7 46605
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 1.78 1.81
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 4GZB 1.78 46.78 44242 2322 97.62 0.1778 0.1766 0.1863 0.20028 0.2071 RANDOM 38.297
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.23 r_dihedral_angle_4_deg 18.527 r_dihedral_angle_3_deg 14.957 r_long_range_B_other 7.779 r_long_range_B_refined 7.768 r_scangle_other 6.821 r_dihedral_angle_1_deg 6.757 r_scbond_it 4.617 r_scbond_other 4.608 r_mcangle_other 4.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.23 r_dihedral_angle_4_deg 18.527 r_dihedral_angle_3_deg 14.957 r_long_range_B_other 7.779 r_long_range_B_refined 7.768 r_scangle_other 6.821 r_dihedral_angle_1_deg 6.757 r_scbond_it 4.617 r_scbond_other 4.608 r_mcangle_other 4.122 r_mcangle_it 4.117 r_mcbond_it 3.151 r_mcbond_other 3.131 r_angle_refined_deg 1.548 r_angle_other_deg 0.989 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 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 2843 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing