8B4N
X-ray structure of phycoerythrin from Porphyridium cruentum
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | PE crystals were grown by hanging drop vapor diffusion method (Russo Krauss et al., 2013) using a drop containing 10 mg/mL PE in 0.250 M ammonium sulphate, 25.0 mM potassium phosphate at pH 5.0, equilibrated with a reservoir containing 0.500 M ammonium sulphate, 50.0 mM potassium phosphate at pH 5.0. |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 186.59 | α = 90 |
b = 186.59 | β = 90 |
c = 59.19 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2022-03-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ELETTRA BEAMLINE 11.2C | 1.00 | ELETTRA | 11.2C |
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 | 1.597 | 46.648 | 99 | 0.101 | 0.107 | 0.035 | 0.997 | 12.9 | 9.2 | 100909 |
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 | 1.597 | 1.625 | 98.3 | 1.028 | 0.999 | 0.36 | 0.595 | 2.2 | 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 3V58 | 1.6 | 46.648 | 100412 | 4971 | 98.994 | 0.223 | 0.2217 | 0.2564 | 23.932 |
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] | |
-0.061 | -0.031 | -0.061 | 0.199 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.983 |
r_dihedral_angle_4_deg | 14.893 |
r_dihedral_angle_3_deg | 13.457 |
r_dihedral_angle_1_deg | 5.821 |
r_lrange_it | 4.18 |
r_lrange_other | 4.143 |
r_scangle_it | 3.373 |
r_scangle_other | 3.368 |
r_mcangle_it | 2.439 |
r_mcangle_other | 2.439 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5070 |
Nucleic Acid Atoms | |
Solvent Atoms | 324 |
Heterogen Atoms | 458 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
autoPROC | data scaling |
PHASER | phasing |