4KOY
Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with Cephalosporin C
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 |
2.41 | 48.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58 | α = 90 |
b = 76.059 | β = 90 |
c = 39.303 | 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 | MARMOSAIC 225 mm CCD | Beryllium Lenses | 2010-07-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | APS | 21-ID-F |
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 | 1.4 | 50 | 100 | 0.045 | 0.045 | 39 | 6 | 34920 | 34920 | -3 | 16.6 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.4 | 1.42 | 100 | 0.548 | 0.548 | 2.5 | 5.7 | 1702 |
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 | 2i6c | 1.4 | 34.94 | 33120 | 33120 | 1754 | 99.86 | 0.14768 | 0.14768 | 0.14632 | 0.17327 | RANDOM | 19.141 |
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] | |
-0.46 | -0.34 | 0.79 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.566 |
r_dihedral_angle_4_deg | 16.119 |
r_dihedral_angle_3_deg | 12.473 |
r_dihedral_angle_1_deg | 5.604 |
r_angle_other_deg | 3.555 |
r_angle_refined_deg | 1.856 |
r_chiral_restr | 0.112 |
r_gen_planes_other | 0.02 |
r_bond_refined_d | 0.019 |
r_gen_planes_refined | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1239 |
Nucleic Acid Atoms | |
Solvent Atoms | 229 |
Heterogen Atoms | 78 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | phasing |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |