4DFE
Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase III from Burkholderia xenovorans
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HN9 | PDB entry 1HN9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 290 | Internal tracking number 228627G11. Crystallant (Wizard III/IV G11): 20% PEG 6000, 0.1 M Hepes pH 7.0, 200 mM NaCl. Protein: BuxeA.00171.c.A1 PW33645 at 35 mg/ml in a buffer consisting of 25 mM HEPES pH 7.0, 300-500 mM NaCl, 2 mM DTT, 0.025% sodium azide, 5% glycerol. Cryoprotection was achieved by supplementing the reservoir solution with 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.23 | 44.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 57.99 | α = 113.72 |
b = 67.03 | β = 89.98 |
c = 89.2 | γ = 100.25 |
Symmetry | |
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Space Group | P 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 | ADSC QUANTUM 315 | 2011-12-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 5.0.1 | 0.9774 | ALS | 5.0.1 |
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 | 2.35 | 50 | 97.8 | 0.087 | 11.9 | 3.3 | 49242 | -3 | 36.372 |
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 | 2.35 | 2.41 | 97.5 | 0.502 | 2.5 | 3.3 |
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 | MR, MR | THROUGHOUT | PDB entry 1HN9 | 2.35 | 50 | 49242 | 2488 | 97.98 | 0.229 | 0.227 | 0.275 | RANDOM | 30.633 |
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] | |
0.12 | -0.43 | -1.09 | -0.37 | 1.88 | 1.61 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.696 |
r_dihedral_angle_4_deg | 19.836 |
r_dihedral_angle_3_deg | 15.564 |
r_dihedral_angle_1_deg | 7.069 |
r_angle_refined_deg | 1.294 |
r_angle_other_deg | 1.167 |
r_chiral_restr | 0.079 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.008 |
r_bond_other_d | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9403 |
Nucleic Acid Atoms | |
Solvent Atoms | 290 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |