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Crystal Structure of GH29 family alpha-L-fucosidase from Fusarium graminearum in the open form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HL8 pdb entry 1HL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 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 30% PEG 2000mme, 0.1M Tris pH 8.0, crystals grow within two days, cryoprotected by Mitegen LV cryo-oil, batch method, temperature 293.15K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.871 α = 105.91 b = 75.887 β = 107.23 c = 80.845 γ = 106.75
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 300 mm CCD 2012-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.56 50 96.9 0.062 11.6 3.9 152745 148010 14.33
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 1.56 1.59 94.4 0.45 3.1 7223
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT pdb entry 1HL8 1.561 41.235 1.97 152931 148005 7210 96.78 0.1364 0.1347 0.1368 0.1691 0.1701 random 19.74
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 20.918 f_angle_d 1.214 f_chiral_restr 0.05 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9251 Nucleic Acid Atoms Solvent Atoms 1786 Heterogen Atoms 272
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction MD2 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing