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VIM-2 metallo-beta-lactamase in complex with 2-(3-fluoro-4-hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid (compound 35)
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, 21-26% (v/v) Polyethylene glycol 3350, 1 mM Tris(2-carboxyethyl)phosphine, 16 mg/mL protein; socked the crystals with 10mM 2-(3-fluoro-4-hydroxyphenyl)-3-oxoisoindoline-4-carboxylic acid
Crystal Properties Matthews coefficient Solvent content 2.09 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.983 α = 90 b = 80.251 β = 130 c = 68.319 γ = 90
Symmetry Space Group C 1 2 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 DECTRIS PILATUS 6M-F 2016-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.17 52.01 100 0.081 0.088 0.034 0.998 8.8 6.6 142903 12.34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.17 1.2 99.9 1.23 1.337 0.517 0.603 6.5 10549
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 1.17 52.01 1.33 140325 7006 98.15 0.1912 0.1902 0.1999 0.2115 0.2173 21.5922
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 13.503 f_angle_d 1 f_chiral_restr 0.085 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3448 Nucleic Acid Atoms Solvent Atoms 481 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction