5KP2
Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae cocrystallized with octanoyl-CoA: hydrolzed ligand
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7 | 289 | 0.2 M ammonium phosphate, 20% PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.39 | 48.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 84.67 | α = 90 |
b = 61.242 | β = 94.67 |
c = 71.524 | 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 | Beryllium Lenses | 2014-03-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.979 | APS | 21-ID-F |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 27 | 96.7 | 0.1 | 0.121 | 0.067 | 6.9 | 2.9 | 48065 |
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 | 2.03 | 96.9 | 0.413 | 2.9 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | THROUGHOUT | 4WZU | 2 | 27 | 45559 | 2360 | 96.64 | 0.19521 | 0.19386 | 0.22095 | RANDOM | 24.408 |
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] | |
0.26 | -0.77 | -0.57 | 0.43 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.635 |
r_dihedral_angle_4_deg | 12.805 |
r_dihedral_angle_3_deg | 11.511 |
r_dihedral_angle_1_deg | 5.959 |
r_long_range_B_refined | 4.978 |
r_long_range_B_other | 4.864 |
r_angle_refined_deg | 1.339 |
r_angle_other_deg | 0.987 |
r_scangle_other | 0.716 |
r_mcangle_it | 0.594 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5283 |
Nucleic Acid Atoms | |
Solvent Atoms | 379 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data collection |
HKL-3000 | data scaling |
MOLREP | phasing |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |