4L8A
Crystal structure of a GNAT superfamily acetyltransferase PA4794 in ternary complex with N-Phenylacetyl-Gly-AcLys and CoA
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2I6C |
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 |
2.4 | 48.75 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.207 | α = 90 |
b = 76.669 | β = 90 |
c = 39.4 | γ = 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 | 2011-10-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.97912 | 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 | 1.2 | 50 | 100 | 0.046 | 0.046 | 62.2 | 8.7 | 55044 | 55044 | -3 | 14.1 |
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 | 1.2 | 1.22 | 100 | 0.564 | 0.564 | 2.8 | 6.1 | 2703 |
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 | 2i6c | 1.2 | 45.85 | 52186 | 52186 | 2787 | 99.97 | 0.1303 | 0.1303 | 0.12893 | 0.15599 | RANDOM | 18.928 |
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] | |
0.45 | -0.17 | -0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 37.124 |
r_dihedral_angle_2_deg | 36.921 |
r_sphericity_bonded | 14.058 |
r_dihedral_angle_4_deg | 13.388 |
r_dihedral_angle_3_deg | 11.414 |
r_rigid_bond_restr | 7.878 |
r_dihedral_angle_1_deg | 5.729 |
r_angle_other_deg | 3.554 |
r_angle_refined_deg | 1.972 |
r_chiral_restr | 0.11 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1236 |
Nucleic Acid Atoms | |
Solvent Atoms | 280 |
Heterogen Atoms | 123 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
HKL-3000 | phasing |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |