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X-ray crystal structure of AmpC beta-lactamase from E. coli in complex with a non-covalent inhibitor 3-[(4-CARBOXYBENZYL)SULFAMOYL]THIOPHENE-2-CARBOXYLIC ACID (compound 4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.7 296 1.7 M potassium phosphate; 3.5 mg/mL AmpC , pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.52 51.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.43 α = 90 b = 76.711 β = 115.61 c = 97.559 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 300 mm CCD 2008-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1 APS 21-ID-D
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 1.9 50 99.9 62237
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 1.9 1.97 100
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 1KE4 1.9 50 59023 3154 99.25 0.17143 0.16925 0.1698 0.21179 0.2115 RANDOM 24.794
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] 1.55 0.48 -0.48 -0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_3_deg 13.241 r_dihedral_angle_4_deg 12.745 r_dihedral_angle_1_deg 5.892 r_scangle_it 3.842 r_scbond_it 2.477 r_mcangle_it 1.593 r_angle_refined_deg 1.453 r_mcbond_it 1.04 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.714 r_dihedral_angle_3_deg 13.241 r_dihedral_angle_4_deg 12.745 r_dihedral_angle_1_deg 5.892 r_scangle_it 3.842 r_scbond_it 2.477 r_mcangle_it 1.593 r_angle_refined_deg 1.453 r_mcbond_it 1.04 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.131 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5457 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling