X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HL8PDB ENTRY 1HL8 (peptide only)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch method8293.151:1 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 coefficientSolvent content
2.0841

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.511α = 105.61
b = 75.512β = 107.19
c = 80.367γ = 106.71
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2013-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.399337.93194.920944019874816
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.39931.42920.5572.33.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1HL8 (peptide only)1.399337.9311.99209440198748190594.90.14490.14470.166721.8
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.77
f_angle_d1.248
f_chiral_restr0.053
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9251
Nucleic Acid Atoms
Solvent Atoms1402
Heterogen Atoms277

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing