2XWD
X-RAY STRUCTURE OF ACID-BETA-GLUCOSIDASE WITH 5N,6O-(N'-(N-OCTYL)IMINO)NOJIRIMYCIN IN THE ACTIVE SITE
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2J25 | PDB ENTRY 2J25 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 6.5 | 0.2M (NH4)2SO4, 0.1 M TRIS PH 6.5, 25% W/V PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.1 | 42 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 68.036 | α = 90 |
b = 96.617 | β = 103.69 |
c = 83.164 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 225 mm CCD | PT COATED SI MIRROR | 2009-06-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-2 | ESRF | ID23-2 |
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 | 2.66 | 29.9 | 99.7 | 0.18 | 12.2 | 7.7 | 28378 | 2 |
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 | 2.66 | 2.72 | 99.4 | 0.55 | 3 | 6.3 |
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 2J25 | 2.66 | 29.92 | 28378 | 1510 | 98.79 | 0.15348 | 0.15003 | 0.21893 | RANDOM | 14.304 |
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] | |
0.03 | -0.01 | -0.02 | -0.02 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.49 |
r_dihedral_angle_4_deg | 20.043 |
r_dihedral_angle_3_deg | 16.24 |
r_dihedral_angle_1_deg | 6.731 |
r_scangle_it | 3.368 |
r_scbond_it | 2.11 |
r_angle_refined_deg | 1.581 |
r_mcangle_it | 1.349 |
r_mcbond_it | 0.689 |
r_chiral_restr | 0.111 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7721 |
Nucleic Acid Atoms | |
Solvent Atoms | 266 |
Heterogen Atoms | 180 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |