4GRX
Structure of an omega-aminotransferase from Paracoccus denitrificans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3GJU | Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU. |
experimental model | PDB | 3I5T | Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU. |
experimental model | PDB | 3HMU | Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU. |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 25 %(w/v) PEG3350, 0.4 M NaCl, 10 mM urea, 0.1 M Tris/HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.41 | 48.93 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.79 | α = 90 |
b = 103.63 | β = 98.88 |
c = 145.43 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | MARMOSAIC 225 mm CCD | Double Crystal | 2009-12-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
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 | 2.6 | 20 | 99.5 | 0.095 | 14.31 | 60091 | 60091 | -3 | -3 | 41.039 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.6 | 2.7 | 99.6 | 0.558 | 2.76 |
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 | Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU. | 2.6 | 19.83 | 60090 | 60090 | 3063 | 99.54 | 0.1809 | 0.1809 | 0.1784 | 0.2274 | RANDOM | 38.2066 |
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] | |
3.75 | -0.03 | -2.41 | -1.35 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.648 |
r_dihedral_angle_4_deg | 18.174 |
r_dihedral_angle_3_deg | 16.208 |
r_dihedral_angle_1_deg | 5.804 |
r_angle_refined_deg | 1.3 |
r_chiral_restr | 0.09 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 14012 |
Nucleic Acid Atoms | |
Solvent Atoms | 245 |
Heterogen Atoms | 20 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
MAR345 | data collection |
XDS | data reduction |