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Fragments bound to the OXA-48 beta-lactamase: Compound 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1M HEPES pH 7.5, 8-12% PEG8000, 4% 1-butanol
Crystal Properties Matthews coefficient Solvent content 2.85 56.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.371 α = 90 b = 107.622 β = 90 c = 124.553 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX-225 2015-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 2.1 45.96 99 0.1608 6.35 3.7 69611 22.2513417337
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 2.1 2.175 100 0.7949 1.54 3.8 6874
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3HBR 2.10000527 45.9606680821 1.33553952209 130998 6568 97.8137180234 0.203233976136 0.200916879833 0.2043 0.246183444911 0.247 Random selection 30.6309030722
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 18.6701818906 f_angle_d 0.495311174818 f_chiral_restr 0.0423515396163 f_bond_d 0.00229749654741 f_plane_restr 0.00158230375386
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7924 Nucleic Acid Atoms Solvent Atoms 1340 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing Aimless data scaling