4PSR
Crystal Structure of alpha-L-fucosidase from Fusarium graminearum in the open form in complex with L-fucose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HL8 | pdb entry 1HL8 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | batch | 8 | 293.15 | 11:1 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, soaked with 50 mM fucose (final concentration) in crystallization solution for around 5 minutes, cryoprotected by Mitegen LV cryo-oil, batch method, temperature 293.15K), flash frozen in liquid nitrogen before data collection. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.13 | 42.28 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.153 | α = 105.69 |
b = 75.989 | β = 107.32 |
c = 80.97 | γ = 106.93 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2012-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.38 | 50 | 96.1 | 0.062 | 9.8 | 3.9 | 223707 | 214983 | 13.54 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.38 | 1.4 | 93.2 | 0.623 | 3 | 10428 |
Refinement
Statistics | |||||||||||||||||||
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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 | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | pdb entry 1HL8 | 1.38 | 43.28 | 1.98 | 223998 | 214971 | 10220 | 95.97 | 0.1397 | 0.1384 | 0.1661 | ramdom | 19.34 |
Temperature Factor Modeling | ||||||
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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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 13.286 |
f_angle_d | 1.381 |
f_chiral_restr | 0.079 |
f_bond_d | 0.011 |
f_plane_restr | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9251 |
Nucleic Acid Atoms | |
Solvent Atoms | 1765 |
Heterogen Atoms | 294 |
Software
Software | |
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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 |