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X-ray structure of the NDM-4 beta-lactamase from Klebsiella pneumonia in complex with 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8SK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 Protein incubated with 10 mM 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid. Precipitant: 18 - 26% (w/v) poly(ethylene glycol) 3350, 2% (v/v) dimethyl sulfoxide, and 100 mM MES (pH 6.0)
Crystal Properties Matthews coefficient Solvent content 2.05 39.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.138 α = 90 b = 59.185 β = 98.5 c = 42.266 γ = 90
Symmetry Space Group P 1 21 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 Bruker PHOTON II 2022-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.3 50 92.7 0.049 16.5 4.8 44587
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.4 77.5 0.286 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.3 32.97 42417 2170 92.68 0.20349 0.20243 0.211 0.22376 0.2325 RANDOM 14.284
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_3_deg 15.656 r_dihedral_angle_2_deg 9.043 r_dihedral_angle_1_deg 7.316 r_long_range_B_refined 5.187 r_long_range_B_other 5.186 r_scangle_other 2.741 r_mcangle_other 2.229 r_mcangle_it 2.228 r_scbond_it 1.926 r_scbond_other 1.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.656 r_dihedral_angle_2_deg 9.043 r_dihedral_angle_1_deg 7.316 r_long_range_B_refined 5.187 r_long_range_B_other 5.186 r_scangle_other 2.741 r_mcangle_other 2.229 r_mcangle_it 2.228 r_scbond_it 1.926 r_scbond_other 1.925 r_mcbond_it 1.534 r_mcbond_other 1.528 r_angle_refined_deg 1.364 r_angle_other_deg 0.469 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing