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Crystal structure of PDC-3 beta-lactamase in complex with the boronic acid inhibitor LP-06
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 273 100 mM Imidazole pH 7.0, 2-8% isopropyl alcohol (IPA), and 16-34% PEG 3350. Protein was in 10 mM HEPES pH 7.5, 150 mM NaCl and 5% glycerol
Crystal Properties Matthews coefficient Solvent content 1.97 37.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.828 α = 90 b = 71.667 β = 90 c = 106.729 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 2019-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97933 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 1.35 28 99.7 0.134 0.998 14.8 12.8 76325
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 1.35 1.38 96.1 0.626 0.896 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.35 28 72326 3919 99.69 0.1309 0.1292 0.1615 0.1793 RANDOM 11.046
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] -0.11 0.02 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.605 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 6.408 r_angle_refined_deg 1.605 r_angle_other_deg 1.493 r_rigid_bond_restr 1.285 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.605 r_dihedral_angle_4_deg 15.149 r_dihedral_angle_3_deg 12.894 r_dihedral_angle_1_deg 6.408 r_angle_refined_deg 1.605 r_angle_other_deg 1.493 r_rigid_bond_restr 1.285 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2781 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling MOLREP phasing