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Crystal structure of AmpC beta-lactamase in complex with fragment 5 (N-{[3-(2-chlorophenyl)-5-methyl-1,2-oxazol-4-yl]carbonyl}glycine)
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 VAPOR DIFFUSION, HANGING DROP 8.8 293 1.7 M potassium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.08 α = 90 b = 76.86 β = 116.26 c = 97.71 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 80 CCD ADSC QUANTUM 315r 2012-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.115869 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 1.35 45.452 97 0.04 18.11 166574 -3 21.398
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 1.35 1.39 95.4 0.482 3.71
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.35 45.452 1.99 166554 6366 97.14 0.1359 0.1351 0.1355 0.1564 0.1562 17.662
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.68 f_angle_d 1.334 f_chiral_restr 0.085 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5524 Nucleic Acid Atoms Solvent Atoms 877 Heterogen Atoms 60
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing