8GYF
Crystal structure of a bright green fluorescent protein (StayGold) with single mutation (K192Y) in jellyfish Cytaeis uchidae from Biortus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 0.2 M Ammonium formate, 20% PEG 3350 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.75 | 55.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 134.707 | α = 90 |
b = 134.707 | β = 90 |
c = 58.568 | γ = 120 |
Symmetry | |
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Space Group | P 61 |
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 EIGER X 9M | 2022-09-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | CLSI BEAMLINE 08ID-1 | 0.946418 | CLSI | 08ID-1 |
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 | 44.235 | 98.8 | 0.261 | 7.9 | 9.3 | 40718 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 2 | 2.05 | 1.097 | 2.4 |
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 | AF2 predicted | 2 | 44.235 | 40712 | 1969 | 98.811 | 0.194 | 0.1916 | 0.2361 | 16.374 |
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] | |
0.459 | 0.23 | 0.459 | -1.491 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.214 |
r_dihedral_angle_4_deg | 14.094 |
r_dihedral_angle_3_deg | 13.095 |
r_dihedral_angle_1_deg | 7.784 |
r_lrange_it | 5.588 |
r_lrange_other | 5.288 |
r_scangle_it | 1.967 |
r_scangle_other | 1.966 |
r_mcangle_it | 1.716 |
r_mcangle_other | 1.716 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3424 |
Nucleic Acid Atoms | |
Solvent Atoms | 625 |
Heterogen Atoms | 46 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |