4OAE
Crystal structure of a GNAT superfamily acetyltransferase PA4794 C29A/C117A/Y128A mutant in complex with chloramphenicol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4KUA | PDB ENTRY 4KUA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | 2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.2 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 57.88 | ¦Á = 90 |
b = 75.626 | ¦Â = 90 |
c = 39.482 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | ADSC QUANTUM 315r | mirrors | 2012-11-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.91837 | APS | 19-ID |
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 | 1.25 | 50 | 99.9 | 0.053 | 0.053 | 43.7 | 7.3 | 48658 | 48658 | -3 | 13.6 |
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 | 1.25 | 1.27 | 100 | 0.747 | 0.747 | 2.4 | 6.3 | 2440 |
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 | PDB ENTRY 4KUA | 1.25 | 45.96 | 46151 | 46151 | 2456 | 99.92 | 0.1221 | 0.1221 | 0.12037 | 0.15476 | RANDOM | 19.185 |
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] | |
-0.42 | -0.85 | 1.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 42.413 |
r_dihedral_angle_2_deg | 34.3 |
r_dihedral_angle_4_deg | 17.615 |
r_sphericity_bonded | 17.322 |
r_dihedral_angle_3_deg | 11.088 |
r_rigid_bond_restr | 8.645 |
r_dihedral_angle_1_deg | 5.667 |
r_long_range_B_other | 5.334 |
r_long_range_B_refined | 5.331 |
r_scangle_other | 4.818 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1239 |
Nucleic Acid Atoms | |
Solvent Atoms | 242 |
Heterogen Atoms | 102 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |