7YCB
HYDROXYNITRILE LYASE FROM THE MILLIPEDE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.5 | 293.15 | 0.1 M BIS-TRIS, 2.0 M ammonium sulfate, incubated in 25% glycerol with a drop of benzaldehyde and 2 M potassium cyanide |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.49 | 64.8 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 123.16 | ¦Á = 90 |
b = 123.16 | ¦Â = 90 |
c = 130.14 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 63 |
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 | IMAGE PLATE | RIGAKU | 2017-08-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU | 1.5418 |
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 | 2.01 | 61.58 | 99.9 | 0.069 | 7.9 | 3 | 74529 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2.01 | 2.05 | 0.069 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6KFE | 2.01 | 49.396 | 74513 | 3631 | 99.893 | 0.208 | 0.2061 | 0.2349 | 39.04 |
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] | |
0.323 | 0.162 | 0.323 | -1.049 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_6_deg | 16.57 |
r_dihedral_angle_3_deg | 14.696 |
r_dihedral_angle_2_deg | 10.637 |
r_dihedral_angle_1_deg | 7.923 |
r_lrange_other | 7.827 |
r_lrange_it | 7.824 |
r_scangle_it | 6.165 |
r_scangle_other | 5.907 |
r_mcangle_it | 4.807 |
r_mcangle_other | 4.806 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5072 |
Nucleic Acid Atoms | |
Solvent Atoms | 339 |
Heterogen Atoms | 125 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
Coot | model building |