4IID
Crystal structure of beta-glucosidase 1 from Aspergillus aculeatus in complex with 1-deoxynojirimycin
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.8 | 293 | 35% MPD, 0.1M Na-acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.05 | 59.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.452 | α = 90 |
b = 121.599 | β = 90 |
c = 221.805 | γ = 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 QUANTUM 270 | 2010-05-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE AR-NE3A | 1.0 | Photon Factory | AR-NE3A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2.3 | 50 | 99.9 | 0.108 | 10.8 | 7.3 | 99751 | 99594 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.3 | 2.34 | 98.7 | 0.444 | 2.4 | 6.3 | 4848 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | FOURIER SYNTHESIS | THROUGHOUT | 2.3 | 39.07 | 94727 | 94197 | 4949 | 99.44 | 0.1579 | 0.1579 | 0.15529 | 0.20675 | RANDOM | 22.806 |
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] | |
0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.352 |
r_dihedral_angle_4_deg | 16.88 |
r_dihedral_angle_3_deg | 14.065 |
r_dihedral_angle_1_deg | 6.508 |
r_angle_refined_deg | 2.04 |
r_chiral_restr | 0.128 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.009 |
r_bond_other_d | |
r_angle_other_deg |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 12762 |
Nucleic Acid Atoms | |
Solvent Atoms | 954 |
Heterogen Atoms | 1066 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
MOLREP | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |