☰ Navigation Tabs
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 VAPOR DIFFUSION, HANGING DROP 8.5 294 400 mM KPi at pH 8.5 with 25% PEG 3350, at 294K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.508 α = 90 b = 76.811 β = 116.66 c = 98.005 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 2008-06-21 M SINGLE WAVELENGTH
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 2.4 50 99.6 0.133 3.6 30971
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) 2.4 2.49 96.8 0.524 3.1 3002
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1KE4 2.49 45.27 27340 1368 99.22 0.196 0.193 0.192 0.252 0.2493 RANDOM 41.99
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] 0.22 0.39 -0.08 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 15.722 r_dihedral_angle_3_deg 15.684 r_dihedral_angle_1_deg 6.23 r_scangle_it 2.364 r_scbond_it 1.73 r_angle_refined_deg 1.409 r_mcangle_it 1.021 r_mcbond_it 0.769 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 15.722 r_dihedral_angle_3_deg 15.684 r_dihedral_angle_1_deg 6.23 r_scangle_it 2.364 r_scbond_it 1.73 r_angle_refined_deg 1.409 r_mcangle_it 1.021 r_mcbond_it 0.769 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.288 r_nbd_refined 0.226 r_chiral_restr 0.186 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5771 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 84
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction