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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 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.109 α = 90 b = 76.177 β = 116.51 c = 97.522 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 WAVELEGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1 ALS 8.3.1
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 1.8 61.8 0.073 3 58911
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 0.457 2.4 3
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 58.12 58911 3130 86.5 0.208 0.207 0.2063 0.226 0.2259 20.64
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 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_4_deg 11.722 r_dihedral_angle_1_deg 5.288 r_angle_refined_deg 1.021 r_scangle_it 0.54 r_mcangle_it 0.439 r_scbond_it 0.396 r_nbtor_refined 0.298 r_mcbond_it 0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_dihedral_angle_3_deg 13.155 r_dihedral_angle_4_deg 11.722 r_dihedral_angle_1_deg 5.288 r_angle_refined_deg 1.021 r_scangle_it 0.54 r_mcangle_it 0.439 r_scbond_it 0.396 r_nbtor_refined 0.298 r_mcbond_it 0.276 r_nbd_refined 0.177 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.083 r_xyhbond_nbd_refined 0.075 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 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 5847 Nucleic Acid Atoms Solvent Atoms 658 Heterogen Atoms 68
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing