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di-Zinc VIM-5 metallo-beta-lactamase in complex with (1-chloro-4-hydroxyisoquinoline-3-carbonyl)-D-tryptophan (Compound 1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A87
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 20% (w/v) Polyethylene glycol 3350,pH=6.5
Crystal Properties Matthews coefficient Solvent content 1.9 35.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.471 α = 90 b = 81.54 β = 90 c = 95.892 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 PILATUS 6M-F 2016-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.987 Diamond I04
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 1.957 81.54 99.7 0.152 14.3 2.2 31417 25.27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.957 2.027 99 0.152 0.062
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 5A87 1.957 62.118 1.33 31256 1999 99.19 0.1906 0.1874 0.1988 0.2372 0.2436 33.7312
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 16.261 f_angle_d 1.075 f_chiral_restr 0.067 f_bond_d 0.016 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3209 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-3000 data reduction