2VC9
Family 89 Glycoside Hydrolase from Clostridium perfringens in complex with 2-acetamido-1,2-dideoxynojirmycin
X-RAY DIFFRACTION
Crystallization
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.84 | 56.38 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 90.96 | ¦Á = 90 |
b = 90.96 | ¦Â = 90 |
c = 252.4 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 |
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 | 113.15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE |
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 | 2.36 | 19.83 | 90.7 | 0.13 | 3.27 | 42780 | 2 |
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 | OTHER | THROUGHOUT | NONE | 2.36 | 19.7 | 41573 | 2198 | 90.7 | 0.205 | 0.203 | 0.246 | RANDOM | 34.49 |
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] | |
1.06 | 0.53 | 1.06 | -1.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.909 |
r_dihedral_angle_4_deg | 18.012 |
r_dihedral_angle_3_deg | 15.575 |
r_dihedral_angle_1_deg | 5.915 |
r_scangle_it | 1.759 |
r_angle_refined_deg | 1.157 |
r_scbond_it | 1.084 |
r_mcangle_it | 0.702 |
r_mcbond_it | 0.373 |
r_nbtor_refined | 0.305 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7151 |
Nucleic Acid Atoms | |
Solvent Atoms | 381 |
Heterogen Atoms | 27 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |