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Crystal structure of a bacterial fucosidase with iminosugar (2S,3S,4R,5S)-3,4-dihydroxy-2-[2'-phenyl]ethynyl-5-methylpyrrolidine
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 291.15 0.16 M AS,
14% PEG 6000
0.1 M imidazole
Crystal Properties Matthews coefficient Solvent content 2.55 51.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.37 α = 90 b = 188.28 β = 94.1 c = 97.93 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 DECTRIS PILATUS 2M 2012-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.77 39.25 95.9 0.111 0.062 6 4 187759
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 1.77 1.8 96.7 1.72 0.969 0.7 4 9353
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.77 39.25 187634 9469 95.75 0.2255 0.2236 0.2299 0.2604 0.2639 RANDOM 35.533
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] 2.48 -0.62 0.33 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.424 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_1_deg 5.68 r_mcangle_it 3.832 r_mcbond_it 2.767 r_mcbond_other 2.766 r_angle_refined_deg 1.448 r_angle_other_deg 1.087 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.424 r_dihedral_angle_4_deg 19.002 r_dihedral_angle_3_deg 14.009 r_dihedral_angle_1_deg 5.68 r_mcangle_it 3.832 r_mcbond_it 2.767 r_mcbond_other 2.766 r_angle_refined_deg 1.448 r_angle_other_deg 1.087 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14157 Nucleic Acid Atoms Solvent Atoms 588 Heterogen Atoms 124
Software Software Software Name Purpose iMOSFLM data reduction PDB_EXTRACT data extraction REFMAC refinement Aimless data scaling