3OYT
1.84 Angstrom resolution crystal structure of 3-oxoacyl-(acyl carrier protein) synthase I (fabB) from Yersinia pestis CO92
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 295 | Crystallization condition: 20%PEG 8K, 0.05M K dihydrogen Phosphate. Paratone-N was used as cryoprotectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.11 | 41.65 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 109.649 | α = 90 |
b = 114.613 | β = 90 |
c = 59.157 | 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 300 mm CCD | Be Lenses/Diamond Laue Mono | 2010-07-31 | M | SINGLE WAVELENGTH | |||||
2 | 1 | x-ray | 100 | CCD | MAR CCD | Mirror | 2010-08-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-G | 0.97856 | APS | 21-ID-G |
2 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.77483 | APS | 21-ID-D |
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 | 1.84 | 30 | 99.6 | 0.127 | 13.13 | 5.7 | 64383 | 64383 | -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) | |||||||||||
1.84 | 1.88 | 97.3 | 0.592 | 2.55 | 4.9 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | SAD model of the data set collected on 21-ID-G | 1.84 | 29.58 | 61048 | 61048 | 3270 | 98.95 | 0.15727 | 0.15536 | 0.19294 | RANDOM | 19.043 |
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] | |
-0.98 | 2.25 | -1.27 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 32.282 |
r_dihedral_angle_4_deg | 10.665 |
r_dihedral_angle_3_deg | 9.191 |
r_scangle_it | 3.474 |
r_scbond_it | 2.358 |
r_dihedral_angle_1_deg | 2.255 |
r_angle_refined_deg | 1.659 |
r_mcangle_it | 1.152 |
r_angle_other_deg | 0.873 |
r_mcbond_it | 0.616 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5924 |
Nucleic Acid Atoms | |
Solvent Atoms | 651 |
Heterogen Atoms | 125 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHENIX | model building |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |