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Crystal Structure of GH29 family alpha-L-fucosidase from Fusarium graminearum in the closed form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HL8 PDB ENTRY 1HL8 (peptide only)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 batch method 8 293.15 1:1 v/v mixture of 14-16 mg/ml alpha-L-fucosidase (stored in 25mM Tris pH 7.5 and partially deglycosylated by incubation 10:1:1 v/v ratio with EndoH and 500 mM sodium citrate pH 5.5 buffer from New England Biolabs for more than 24hrs before setting up the drop) with 40% PEG 2000mme, 0.1M Tris pH 8.0, crystals grow within two days, cryoprotected by Mitegen LV cryo-oil, batch method, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.511 α = 105.61 b = 75.512 β = 107.19 c = 80.367 γ = 106.71
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 MARMOSAIC 225 mm CCD 2013-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3993 37.931 94.9 209440 198748 16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3993 1.42 92 0.557 2.3 3.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1HL8 (peptide only) 1.3993 37.931 1.99 209440 198748 1905 94.9 0.1449 0.1447 0.1468 0.1667 0.1699 21.8
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 12.77 f_angle_d 1.248 f_chiral_restr 0.053 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9251 Nucleic Acid Atoms Solvent Atoms 1402 Heterogen Atoms 277
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MD2 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing