5HY2
Structure-function analysis of functionally diverse members of the cyclic amide hydrolase family of Toblerone fold enzymes
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5HY0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 281 | Protein was at 2.7 mg/mL with added atrazine; reservoir was 22% PEG 3350, 86 mM sodium acetate; drops were 150 nL protein plus 140 nL reservoir plus 10 nL microseeds. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.09 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 93.297 | ¦Á = 90 |
b = 72.75 | ¦Â = 92.22 |
c = 133.054 | ¦Ã = 90 |
Symmetry | |
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Space Group | I 1 2 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 | ADSC QUANTUM 315r | 2015-02-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.97070 | Australian Synchrotron | MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.6 | 46.6 | 99.9 | 14 | 7.5 | 27567 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.6 | 2.72 | 99.1 | 2.1 | 7.4 |
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 | 5HY0 | 2.6 | 41.5 | 26209 | 1354 | 99.85 | 0.20403 | 0.20217 | 0.24123 | RANDOM | 54.402 |
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] | |
-0.94 | -1.97 | 4.35 | -3.25 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 31.997 |
r_dihedral_angle_4_deg | 20.962 |
r_dihedral_angle_3_deg | 15.888 |
r_long_range_B_other | 11.565 |
r_long_range_B_refined | 11.564 |
r_scangle_other | 7.241 |
r_mcangle_it | 7.203 |
r_mcangle_other | 7.203 |
r_dihedral_angle_1_deg | 5.841 |
r_scbond_it | 4.644 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4719 |
Nucleic Acid Atoms | |
Solvent Atoms | 31 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |