4IW7
Crystal structure of 8-amino-7-oxononanoate synthase (bioF) from Francisella tularensis.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2G6W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.5 | 289 | 0.7 M Sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.16 | 42.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 113.486 | α = 90 |
b = 113.486 | β = 90 |
c = 158.128 | γ = 120 |
Symmetry | |
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Space Group | H 3 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 lens | 2012-11-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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 | 2.25 | 50 | 100 | 0.079 | 29.7 | 8.9 | 18866 | 18866 | -3 |
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 | 2.25 | 2.29 | 100 | 0.742 | 2.1 | 8.5 |
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 | 2G6W | 2.25 | 41.77 | 17890 | 17890 | 969 | 99.97 | 0.18828 | 0.18828 | 0.18571 | 0.23836 | RANDOM | 49.73 |
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] | |
-2.36 | -2.36 | -2.36 | 7.66 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.02 |
r_dihedral_angle_4_deg | 22.203 |
r_dihedral_angle_3_deg | 16.767 |
r_dihedral_angle_1_deg | 5.772 |
r_angle_refined_deg | 1.536 |
r_angle_other_deg | 0.838 |
r_chiral_restr | 0.088 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2615 |
Nucleic Acid Atoms | |
Solvent Atoms | 110 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | phasing |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |