8CXA
Crystal Structure of 3-oxoacyl-[acyl-carrier-protein] reductase from Mycobacterium smegmatis with bound NAD
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 290 | Protein at 28.58 mg/mL was mixed 1:1 (0.4 uL protein and 0.4 uL precipitant) with 12.5% w/v PEG 1000, 12.5% w/v PEG3350, 12.5% v/v MPD, 0.03M magnesium chloride, 0.03M calcium chloride, and 0.1M MOPS/HEPES-Na pH 7.5 (Morpheus A8). Tray: 320494. Cryo: Direct. Puck: ndu6-9 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.03 | 39.33 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.86 | α = 90 |
b = 128.78 | β = 96.03 |
c = 60.9 | 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 | RAYONIX MX-300 | Beryllium Lenses | 2022-04-08 | 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) | Rrim I (All) | CC (Half) | 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 | 1.65 | 45.25 | 99.1 | 0.04 | 0.047 | 0.999 | 15.41 | 3.11 | 110664 | 21.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.65 | 1.69 | 96.7 | 0.413 | 0.515 | 0.858 | 2.18 | 2.693 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 2ew8 | 1.65 | 45.25 | 1.35 | 110620 | 2073 | 99.04 | 0.1578 | 0.1574 | 0.1822 | 29.3377 |
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] | |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7404 |
Nucleic Acid Atoms | |
Solvent Atoms | 778 |
Heterogen Atoms | 88 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | phasing |