5XYT
Structure of 6-aminohexanoate-oligomer hydrolase from Arthrobacter sp. KI72., H130Y mutant
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 1.2-2.2 M ammonium sulphate, 0.2 M NaCl, 0.1 M HEPES buffer pH 7.5-8.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 44.12 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.232 | α = 90 |
b = 144.616 | β = 90 |
c = 128.184 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 RAXIS VII | 2008-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 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 | 1.9 | 100 | 96.5 | 0.04 | 14.9 | 2.78 | 49919 |
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 | 1.9 | 1.97 | 75.6 | 0.124 | 6 | 2.05 |
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 | 5XYG | 1.9 | 72.31 | 47363 | 2549 | 96.46 | 0.16099 | 0.15884 | 0.201 | RANDOM | 20.99 |
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] | |
2.96 | -1.67 | -1.29 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.98 |
r_dihedral_angle_4_deg | 16.752 |
r_dihedral_angle_3_deg | 14.307 |
r_dihedral_angle_1_deg | 7.621 |
r_scangle_it | 7.265 |
r_scbond_it | 5.488 |
r_mcangle_it | 3.361 |
r_mcbond_it | 2.405 |
r_angle_refined_deg | 1.001 |
r_chiral_restr | 0.09 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4869 |
Nucleic Acid Atoms | |
Solvent Atoms | 390 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
d*TREK | data reduction |
d*TREK | data scaling |
PHASER | phasing |