☰ Navigation Tabs
VIM-2 metallo-beta-lactamase in complex with 3-oxo-2-phenylisoindoline-4-carboxylic acid (compound 30)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M Magnesium Formate, 21% (v/v) Polyethylene glycol 3350, 5 mM 3-oxo-2-phenylisoindoline-4-carboxylic acid, 16 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 1.83 32.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.46 α = 90 b = 65.637 β = 90 c = 70.721 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 CCD RIGAKU SATURN 944+ OSMIC HF 2016-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.86 50 99.6 0.058 0.062 0.024 18.2 6.7 16377 14.94
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 1.86 1.93 97.9 0.163 5.7
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 4C1D 1.86 24.055 1.34 16334 1623 99.63 0.1303 0.1266 0.1438 0.1642 0.178 15.2723
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 12.667 f_angle_d 0.771 f_chiral_restr 0.052 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1653 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 34
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction CrystalClear data reduction HKL-3000 phasing