3DYI
Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | hanging drop | 6 | 298 | PEG 8000, Na acetate, pH 6.0, hanging drop, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.6 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.442 | α = 90 |
b = 47.442 | β = 90 |
c = 174.18 | γ = 120 |
Symmetry | |
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Space Group | P 32 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 | 120 | IMAGE PLATE | RIGAKU RAXIS IV | Osmic Blue | 2006-12-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 | 1.54 |
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 | 1.6 | 33.54 | 94.4 | 0.048 | 14.5 | 4.4 | 31093 | 29366 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3DKR | 1.72 | 33.54 | 25016 | 24097 | 1241 | 95.84 | 0.178 | 0.178 | 0.177 | 0.201 | RANDOM | 25.404 |
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] | |
0.33 | 0.16 | 0.33 | -0.49 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.822 |
r_dihedral_angle_4_deg | 15.923 |
r_dihedral_angle_3_deg | 11.56 |
r_dihedral_angle_1_deg | 5.199 |
r_scangle_it | 1.741 |
r_scbond_it | 1.131 |
r_angle_refined_deg | 1.03 |
r_mcangle_it | 0.688 |
r_mcbond_it | 0.405 |
r_nbtor_refined | 0.304 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1837 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
CrystalClear | data collection |
CrystalClear | data reduction |