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Crystal structure of AmpC beta-lactamase in complex with fragment 20 (1,3-diethyl-2-thioxodihydropyrimidine-4,6(1H,5H)-dione)
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 2.55 51.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.61 α = 90 b = 77.8 β = 116.59 c = 98.69 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 2012-05-31 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 2.28 29.857 88.8 0.032 28.12 32352 -3 27.38
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 2.28 2.34 98.2 0.106 10.72
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 2.282 29.857 1.99 32348 1224 89.03 0.1626 0.1606 0.1619 0.2127 0.2143 21.3009
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 12.277 f_angle_d 0.93 f_chiral_restr 0.036 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5424 Nucleic Acid Atoms Solvent Atoms 410 Heterogen Atoms 57
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing