3PPL
Crystal structure of an aspartate transaminase (NCgl0237, Cgl0240) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 1.25 A resolution
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 293 | 0.2M sodium chloride, 20.0% polyethylene glycol 8000, 0.1M phosphate-citrate pH 4.2, Additive: 0.001 M alpha-ketoglutaric acid, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.44 | 49.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.755 | α = 90 |
b = 54.424 | β = 101.6 |
c = 176.34 | γ = 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 | MARMOSAIC 325 mm CCD | 2010-02-11 | M | MAD |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRL BEAMLINE BL11-1 | 0.91837,0.97944,0.97908 | SSRL | BL11-1 |
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 | 1.25 | 29.324 | 92.1 | 0.035 | 13.04 | 3.6 | 241991 | -3 | 10.292 |
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 | 1.25 | 1.29 | 84.8 | 0.276 | 2.75 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | MAD | THROUGHOUT | 1.25 | 29.324 | 241986 | 12140 | 96.56 | 0.1059 | 0.1049 | 0.1242 | RANDOM | 14.5267 |
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] | |
0.17 | 0.16 | 0.2 | -0.31 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.581 |
r_dihedral_angle_4_deg | 12.842 |
r_dihedral_angle_3_deg | 11.128 |
r_sphericity_free | 8.924 |
r_dihedral_angle_1_deg | 5.991 |
r_scangle_it | 4.789 |
r_sphericity_bonded | 4.085 |
r_scbond_it | 3.231 |
r_mcangle_it | 2.178 |
r_angle_refined_deg | 1.598 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6483 |
Nucleic Acid Atoms | |
Solvent Atoms | 1228 |
Heterogen Atoms | 66 |
Software
Software | |
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Software Name | Purpose |
SHELX | phasing |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |