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Crystal structure of a bacterial fucosidase with iminosugar inhibitor (2S,3S,4R,5S)-2-[N-(methylferrocene)]aminoethyl-5-methylpyrrolidine-3,4-diol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291.5 0.13M ammonium sulfate, 16% PEG 6K, 0.1M imidazole pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.54 α = 90 b = 187.001 β = 94.19 c = 97.671 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 2M 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91730 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.714 97.409 96.7 0.072 10.9 4 155289 155289
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.98 95 0.434 0.434 1.7 3.5 22278
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WVV 1.88 97.409 155289 155246 7806 96.58 0.1915 0.1899 0.1969 0.2219 0.2282 AS 2WVV 31.1146
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] 1.3 -0.31 -0.33 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.575 r_dihedral_angle_4_deg 19.818 r_dihedral_angle_3_deg 13.437 r_dihedral_angle_1_deg 5.872 r_mcangle_it 3.668 r_mcbond_it 2.802 r_mcbond_other 2.802 r_angle_refined_deg 1.659 r_angle_other_deg 1.32 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.575 r_dihedral_angle_4_deg 19.818 r_dihedral_angle_3_deg 13.437 r_dihedral_angle_1_deg 5.872 r_mcangle_it 3.668 r_mcbond_it 2.802 r_mcbond_other 2.802 r_angle_refined_deg 1.659 r_angle_other_deg 1.32 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.009 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14109 Nucleic Acid Atoms Solvent Atoms 732 Heterogen Atoms 172
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing