7ZSF
Structure of Orange Carotenoid Protein with canthaxanthin bound
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4XB5 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.5 | 293 | 100 mM sodium acetate pH 4.5, 10 % poly-ethylene glycol 20,000, 3 % glycerol |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.5 | 50.89 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.569 | α = 90 |
b = 82.569 | β = 90 |
c = 87.365 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | PIXEL | DECTRIS EIGER2 XE 16M | 2019-07-04 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 50 | PIXEL | DECTRIS PILATUS 12M | 2020-07-29 | M | SINGLE WAVELENGTH | ||||||
3 | 1 | x-ray | 50 | PIXEL | DECTRIS PILATUS 12M | 2020-07-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9796 | Diamond | I03 |
2 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 4.42801 | Diamond | I23 |
3 | SYNCHROTRON | DIAMOND BEAMLINE I23 | 4.27532 | Diamond | I23 |
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) | 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 | 1.36 | 87.29 | 99.97 | 0.075 | 0.079 | 0.025 | 17.1 | 19.9 | 74252 |
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) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.36 | 1.4 | 100 | 3.543 | 3.48 | 0.779 | 0.519 | 1.1 | 19.9 |
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 | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4XB5 | 1.36 | 55.396 | 74207 | 3699 | 99.884 | 0.19 | 0.189 | 0.2179 | RANDOM | 25.954 |
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] | |
0.001 | 0.001 | -0.003 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.514 |
r_dihedral_angle_4_deg | 16.814 |
r_dihedral_angle_3_deg | 12.579 |
r_lrange_it | 7.807 |
r_dihedral_angle_1_deg | 5.822 |
r_scangle_it | 4.593 |
r_scbond_it | 3.173 |
r_mcangle_it | 3.096 |
r_mcbond_it | 2.152 |
r_angle_refined_deg | 1.957 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2376 |
Nucleic Acid Atoms | |
Solvent Atoms | 388 |
Heterogen Atoms | 53 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
DIALS | data reduction |
DIALS | data scaling |
MOLREP | phasing |
SHELXCD | phasing |