7QHV
Crystal structure of the sulfoquinovosyl binding protein SmoF complexed with sulfoquinovosyl diacylglycerol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7QHU | D_1292119394 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 279 | 0.2M L-Na-glutamate, alanine, glycine, lysine hydrochloride, serine, 0.1M TRIS, bicine, 12.5% MPD, PEG1000, PEG3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.2 | 43.98 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 53.215 | α = 90 |
b = 69.589 | β = 91.539 |
c = 104.574 | 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 | 210 | PIXEL | DECTRIS PILATUS 6M-F | 2019-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.97933 | Diamond | I04 |
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) | 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 | 2.14 | 69.59 | 99.9 | 0.093 | 0.124 | 0.081 | 0.992 | 8.9 | 4.1 | 42301 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.14 | 2.2 | 0.305 | 0.406 | 0.265 | 0.942 | 4.1 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | D_1292119394 | 2.14 | 57.995 | 42277 | 2124 | 99.865 | 0.206 | 0.2035 | 0.2598 | 24.287 |
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] | |
3.124 | 3.128 | -0.769 | -2.52 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.392 |
r_dihedral_angle_4_deg | 22.688 |
r_dihedral_angle_3_deg | 14.801 |
r_dihedral_angle_1_deg | 6.61 |
r_lrange_it | 4.222 |
r_lrange_other | 4.204 |
r_scangle_it | 2.884 |
r_scangle_other | 2.883 |
r_mcangle_it | 2.553 |
r_mcangle_other | 2.553 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5828 |
Nucleic Acid Atoms | |
Solvent Atoms | 208 |
Heterogen Atoms | 73 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
REFMAC | refinement |
Aimless | data scaling |
MOLREP | phasing |