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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, temperature 294.0K
Crystal Properties Matthews coefficient Solvent content 2.49 50.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.346 α = 90 b = 74.655 β = 116.58 c = 98.948 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 45.189 99.2 71462
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 1.9 97.4 0.445 1.2
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 38.69 71430 3573 99.2 0.191 0.19 0.1892 0.218 0.2169 18.11
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 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.759 r_dihedral_angle_3_deg 13.515 r_dihedral_angle_4_deg 11.716 r_dihedral_angle_1_deg 5.724 r_angle_refined_deg 1.09 r_scangle_it 1.059 r_scbond_it 0.783 r_mcangle_it 0.682 r_mcbond_it 0.474 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.759 r_dihedral_angle_3_deg 13.515 r_dihedral_angle_4_deg 11.716 r_dihedral_angle_1_deg 5.724 r_angle_refined_deg 1.09 r_scangle_it 1.059 r_scbond_it 0.783 r_mcangle_it 0.682 r_mcbond_it 0.474 r_nbtor_refined 0.299 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.132 r_xyhbond_nbd_refined 0.08 r_chiral_restr 0.072 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 5824 Nucleic Acid Atoms Solvent Atoms 797 Heterogen Atoms 44
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction