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AmpC beta-lactamase in complex with Fragment-based Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KE4 PDB entry 1KE4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.7 294 1.7M potassium phosphate, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.52 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.525 α = 90 b = 76.547 β = 116.36 c = 98.009 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 ADSC QUANTUM 210 2008-01-25 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
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 1.8 50 98.7 72028
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) 1.8 1.86 94.1 0.277
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1KE4 1.8 32.44 72028 3612 98.3 0.206 0.205 0.2033 0.229 0.2295 27.79
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] 0.19 0.16 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_3_deg 13.799 r_dihedral_angle_4_deg 12.144 r_dihedral_angle_1_deg 5.81 r_angle_refined_deg 1.16 r_scangle_it 0.845 r_mcangle_it 0.695 r_scbond_it 0.669 r_mcbond_it 0.451 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.938 r_dihedral_angle_3_deg 13.799 r_dihedral_angle_4_deg 12.144 r_dihedral_angle_1_deg 5.81 r_angle_refined_deg 1.16 r_scangle_it 0.845 r_mcangle_it 0.695 r_scbond_it 0.669 r_mcbond_it 0.451 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.208 r_nbd_refined 0.19 r_xyhbond_nbd_refined 0.089 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg 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 5810 Nucleic Acid Atoms Solvent Atoms 520 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction