8R44
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, SITTING DROP | 283 | 0.12 M Ethylene glycols (0.3M diethylene glycol; 0.3M triethylene glycol; 0.3M tetraethylene glycol; 0.3M pentaethylene glycol), 0.1 M Tris (base);BICINE pH 8.5, 30% v/v Precipitant Mix 1 (20% v/v PEG 500 MME; 10 % w/v PEG 20000) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.287 | α = 90 |
b = 111.812 | β = 92.308 |
c = 68.273 | 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 | 40 | PIXEL | DECTRIS PILATUS 6M | 2021-06-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.3 | 0.896 | BESSY | 14.3 |
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 | 1.58 | 43.841 | 99.58 | 0.998 | 12.84 | 3.7 | 112709 |
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 | 1.58 | 1.636 | 0.418 |
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 | 1.58 | 43.841 | 112680 | 5372 | 99.614 | 0.176 | 0.175 | 0.1945 | 28.817 |
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] | |
-0.064 | 0.128 | 0.004 | 0.049 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_3_deg | 16.062 |
r_dihedral_angle_6_deg | 15.482 |
r_lrange_it | 9.361 |
r_lrange_other | 9.309 |
r_dihedral_angle_2_deg | 8.465 |
r_dihedral_angle_1_deg | 6.537 |
r_scangle_it | 6.258 |
r_scangle_other | 6.257 |
r_mcangle_it | 4.613 |
r_mcangle_other | 4.613 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4924 |
Nucleic Acid Atoms | |
Solvent Atoms | 587 |
Heterogen Atoms | 158 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASER | phasing |