8R45
Phytochromobilin-adducted PAS-GAF bidomain of Glycine max phytochrome A
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6TC7 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 283 | 0.04 M Ethylene glycols (0.01M Diethylene glycol; 0.01M Triethylene glycol; 0.01M Tetraethylene glycol; 0.01M Pentaethylene glycol); 0.1 M Tris (base); BICINE pH 9.0; 21% Precipitant Mix (7% v/v MPD; 7% PEG 1000; 7% w/v PEG 3350) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.67 | 53.88 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.542 | α = 90 |
b = 112.526 | β = 92.078 |
c = 68.37 | 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 | 100 | PIXEL | DECTRIS PILATUS 2M | 2021-11-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | 0.9184 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.86 | 42.34 | 99.92 | 0.998 | 12.88 | 6.9 | 70335 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.86 | 1.926 | 0.592 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | 1.86 | 42.34 | 70334 | 3578 | 99.964 | 0.17 | 0.1693 | 0.192 | 31.988 |
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] | |
-0.503 | -0.03 | 0.381 | 0.124 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.205 |
r_dihedral_angle_6_deg | 15.96 |
r_dihedral_angle_2_deg | 9.705 |
r_lrange_it | 8.914 |
r_lrange_other | 8.893 |
r_dihedral_angle_1_deg | 6.74 |
r_scangle_it | 6.464 |
r_scangle_other | 6.463 |
r_mcangle_other | 4.726 |
r_mcangle_it | 4.721 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4979 |
Nucleic Acid Atoms | |
Solvent Atoms | 465 |
Heterogen Atoms | 99 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |