7QCZ
Structure of the orange carotenoid protein from Planktothrix agardhii binding canthaxanthin in the C2 space group
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3MG1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5 | 277 | 0.2 M Bis-Tris pH 5.5, 20%-25% PEG 3550 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 82.01 | α = 90 |
b = 67.5 | β = 117.821 |
c = 61.94 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | IMAGE PLATE | MAR scanner 345 mm plate | 2019-10-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 1.85 | 19.23 | 92.94 | 0.052 | 0.066 | 0.04 | 0.997 | 11.96 | 2.4 | 23806 | 26.48 |
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 | 1.85 | 1.92 | 79.92 | 0.5813 | 0.7392 | 0.4513 | 0.675 | 1.83 | 2.3 |
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 | FREE R-VALUE | 3mg1 | 1.85 | 18.26 | 1.36 | 23803 | 1190 | 92.7 | 0.1787 | 0.1752 | 0.245 | 30.34 |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 8.5402 |
f_angle_d | 0.8543 |
f_chiral_restr | 0.0491 |
f_plane_restr | 0.0091 |
f_bond_d | 0.0046 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2405 |
Nucleic Acid Atoms | |
Solvent Atoms | 427 |
Heterogen Atoms | 42 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PHENIX | refinement |
TRUNCATE | data reduction |
XSCALE | data scaling |
PHASER | phasing |