2W5O
Complex structure of the GH93 alpha-L-arabinofuranosidase of Fusarium graminearum with arabinobiose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2W5N | PDB ENTRY 2W5N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 22% PEG 4K, 100 MM HEPES 7.5, 50 MM AMSO4, 20% GLYCEROL FOR CRYOPROTECTION |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.78 | 55.77 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 48.62 | ¦Á = 90 |
b = 86.88 | ¦Â = 90 |
c = 108.17 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | ADSC CCD | 2008-09-28 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 2.05 | 48.62 | 99.9 | 0.13 | 8.3 | 3.7 | 29532 | 2 |
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 | 2.05 | 2.16 | 99.8 | 0.43 | 2.8 | 3.8 |
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 | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | PDB ENTRY 2W5N | 2.05 | 45.93 | 27981 | 1498 | 99.9 | 0.171 | 0.168 | 0.216 | RANDOM | 14.59 |
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] | |
-0.38 | -0.16 | 0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.661 |
r_dihedral_angle_4_deg | 17.419 |
r_dihedral_angle_3_deg | 12.895 |
r_dihedral_angle_1_deg | 6.993 |
r_scangle_it | 3.066 |
r_scbond_it | 2.029 |
r_angle_refined_deg | 1.584 |
r_mcangle_it | 1.18 |
r_mcbond_it | 0.669 |
r_chiral_restr | 0.101 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2848 |
Nucleic Acid Atoms | |
Solvent Atoms | 318 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |