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Approved Drugs Containing Thiols as Inhibitors of Metallo-beta- lactamases: Strategy To Combat Multidrug-Resistant Bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6X PDB ENTRY 3Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 FOR CRYSTALLIZATION, THE PURIFIED PROTEIN WAS CONCENTRATED TO 19.88 MG/ML. APO - NDM - 1 CRYSTALS WERE GROWN AT 25 C FOR 3 WEEKS USING THE HANGING - DROP VAPOUR DIFFUSION METHOD BY MIXING 0.7UL OF PROTEIN SOLUTION WITH 1UL OF RESERVOIR BUFFER (24 % PEG 1500 AND 0.05 M TBG (SODIUM TARTRATE/BIS - TRIS/GLYCYLGLYCINE) PH 4) AND 0.3UL OF 1/10 DILUTION OF NDM - 1 CRYSTAL SEEDS STOCK.
Crystal Properties Matthews coefficient Solvent content 2.6 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.047 α = 90 b = 108.047 β = 90 c = 92.571 γ = 90
Symmetry Space Group P 41 21 2
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 2014-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 2.6 46.66 100 0.21 12.17 9.2 17411 1.89 41.11
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 2.6 2.69 100 1.25 1.89 9.7
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3Q6X 2.6 46.659 1.23 17404 1614 99.89 0.2103 0.2081 0.2134 0.2518 0.256 47.6
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 12.572 f_angle_d 0.739 f_chiral_restr 0.03 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3520 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing