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Crystal structure of PDC-3 Y221H beta-lactamase in complex with the boronic acid inhibitor S02030
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S22
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. The protein is in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol
Crystal Properties Matthews coefficient Solvent content 1.94 36.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.685 α = 90 b = 71.765 β = 90 c = 104.784 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 PIXEL DECTRIS EIGER X 16M 2020-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97935 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.42 29.62 99.6 0.076 0.999 20.6 13.2 64139
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.46 95.2 0.704 0.883 3 12
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 3S22 1.42 29.62 60901 3163 99.63 0.1475 0.1466 0.1465 0.1642 0.1646 RANDOM 15.346
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 r_dihedral_angle_2_deg 30.87 r_dihedral_angle_4_deg 15.477 r_dihedral_angle_3_deg 13.798 r_dihedral_angle_1_deg 6.72 r_angle_refined_deg 1.65 r_angle_other_deg 1.465 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.87 r_dihedral_angle_4_deg 15.477 r_dihedral_angle_3_deg 13.798 r_dihedral_angle_1_deg 6.72 r_angle_refined_deg 1.65 r_angle_other_deg 1.465 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2778 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing