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Toho-1 Beta Lactamase in complex with Avibactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 Crystals were grown at 20 C using 30 micro litres of 10 mg/ml protein concentration in a solution containing 2.0 M ammonium sulfate and 0.2 M sodium citrate using the batch method.
Crystal Properties Matthews coefficient Solvent content 2.66 53.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.67 α = 90 b = 72.67 β = 90 c = 97.928 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS 6M 2017-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.98 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.15 38.65 97.7 0.99 17.6 5.5 104187 10.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.21 0.89
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.15 36.34 1.34 104187 5022 96.74 0.1344 0.1335 0.1333 0.1512 0.1509 14.82
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 13.5959 f_angle_d 1.0979 f_chiral_restr 0.0766 f_plane_restr 0.0107 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1969 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing