2ZX5
alpha-L-fucosidase complexed with inhibitor, F10
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2ZWZ | PDB enrty 2ZWZ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 298 | 15% PEG 5000 MME, 0.1M HEPES, pH 7.2, 5% Jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.78 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 180.52 | α = 90 |
b = 180.52 | β = 90 |
c = 169.266 | γ = 120 |
Symmetry | |
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Space Group | H 3 2 |
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 | NOIR-1 | mirrors | 2007-06-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.0000 | ALS | 4.2.2 |
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 | 2.65 | 30 | 100 | 0.125 | 10.3 | 11.19 | 30844 | 30844 | 5 |
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) | |||||||||||
2.65 | 2.74 | 100 | 0.501 | 3.5 | 11.3 | 3050 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB enrty 2ZWZ | 2.65 | 30 | 30844 | 30649 | 1521 | 99.4 | 0.1941 | 0.1941 | 0.1908 | 0.2562 | RANDOM | 42.638 |
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] | |
2.618 | -3.265 | 2.618 | -5.236 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.90623 |
c_bond_d | 0.018792 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7278 |
Nucleic Acid Atoms | |
Solvent Atoms | 339 |
Heterogen Atoms | 50 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
CNS | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
CNS | phasing |