3NYT
X-ray crystal structure of the WlbE (WpbE) aminotransferase from pseudomonas aeruginosa, mutation K185A, in complex with the PLP external aldimine adduct with UDP-3-amino-2-N-acetyl-glucuronic acid, at 1.3 angstrom resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3NYS | PDB ENTRY 3NYS |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 25% pentaerythritol propoxylate, 100 mM MES, 50mM UDP-3-amino-20N-acetyl-glucuronic acid, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.08 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 59.684 | ¦Á = 90 |
b = 92.17 | ¦Â = 111.84 |
c = 75.652 | ¦Ã = 90 |
Symmetry | |
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Space Group | C 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 | Bruker Platinum 135 | montel | 2010-01-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU200 | 1.54178 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym 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 | 1.3 | 30 | 97.7 | 0.051 | 0.051 | 15.8 | 5.5 | 90696 | 90696 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.3 | 1.33 | 86.1 | 0.33 | 0.33 | 3 | 2.2 | 3399 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | PDB ENTRY 3NYS | 1.301 | 30 | 90693 | 86156 | 4537 | 97.7 | 0.19097 | 0.19097 | 0.18964 | 0.21626 | RANDOM | 14.137 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.61 | 0.03 | -0.48 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.325 |
r_dihedral_angle_4_deg | 20.342 |
r_dihedral_angle_3_deg | 12.576 |
r_dihedral_angle_1_deg | 6.262 |
r_scangle_it | 5.455 |
r_scbond_it | 3.515 |
r_mcangle_it | 2.288 |
r_angle_refined_deg | 2.18 |
r_mcbond_it | 1.519 |
r_chiral_restr | 0.146 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2729 |
Nucleic Acid Atoms | |
Solvent Atoms | 470 |
Heterogen Atoms | 56 |
Software
Software | |
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Software Name | Purpose |
PROTEUM PLUS | data collection |
PHASER | phasing |
REFMAC | refinement |
SAINT | data reduction |
SADABS | data scaling |