1E4I
2-deoxy-2-fluoro-beta-D-glucosyl/enzyme intermediate complex of the beta-glucosidase from Bacillus polymyxa
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BGA | PDB ENTRY 1BGA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | DROP: 10 MICROL PROTEIN (8 MG/ML)+ 5 MICROL PP(1M, PH=7)+5 MICROL INH (5MM) RESERVOIR: 1.3M PP, pH 7.00 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.1 | 70 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 136.23 | ¦Á = 90 |
b = 136.23 | ¦Â = 90 |
c = 173.26 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 4 2 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 | 1996-10-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM02 | ESRF | BM02 |
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 | 1.96 | 42.3 | 98 | 0.04 | 5 | 56246 |
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 | 2.1 | 95 | 0.34 |
Refinement
Statistics | |||||||||||||||||||
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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 | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1BGA | 2 | 8 | 53692 | 98 | 0.21 | 0.21 | 0.25 | RANDOM | 15.9 |
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 |
x_dihedral_angle_d | 24.9 |
x_improper_angle_d | 1.93 |
x_angle_deg | 1.54 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3644 |
Nucleic Acid Atoms | |
Solvent Atoms | 234 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | refinement |
XDS | data reduction |
XSCALE | data scaling |
AMoRE | phasing |