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Metal Beta Lactamase VIM-2 in Complex with Dual MBL/SBL Inhibitor 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20 mM Tris, 200 mM NaCl, pH7.5
Crystal Properties Matthews coefficient Solvent content 1.86 33.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.642 α = 90 b = 80.073 β = 90 c = 80.104 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 195 PIXEL DECTRIS EIGER R 1M 2024-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 1 SSRF BL19U1
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 1.757 50 99.9 0.9986 22.6 25.05 42746
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 1.76 1.8 0.9211
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 8HX5 1.757 42.879 1.34 42638 1994 99.69 0.2172 0.215 0.2244 0.261 0.2664
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 15.661 f_angle_d 1.106 f_chiral_restr 0.063 f_bond_d 0.028 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3454 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling HKL-3000 data reduction PHASER phasing