6TC7
PAS-GAF bidomain of Glycine max phytochromeA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 283.15 | 0.05 M imidazole, 0.05 M MES, 0.02 M DL-Glutamatic acid monohydrate, 0.02 M DL-Alanine, 0.02M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine, 12% (v/v) Glycerol, 6% (w/v) PEG4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.68 | 54.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 55.423 | α = 90 |
b = 113.233 | β = 93.521 |
c = 68.457 | 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 | PSI PILATUS 6M | 2019-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.9184 | BESSY | 14.1 |
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 | 2.13 | 44.35 | 99.5 | 0.127 | 0.151 | 0.08 | 0.998 | 10 | 6.8 | 46863 | 36.395 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 2.13 | 2.19 | 99.8 | 1.95 | 2.306 | 0.875 | 0.318 | 0.9 | 6.9 |
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 | 6TBY | 2.13 | 44.347 | 46830 | 1866 | 99.399 | 0.191 | 0.1892 | 0.2415 | 48.593 |
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] | |
0.226 | 0.067 | -0.05 | -0.184 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.513 |
r_dihedral_angle_4_deg | 20.255 |
r_dihedral_angle_3_deg | 18.163 |
r_lrange_it | 10.14 |
r_lrange_other | 10.131 |
r_dihedral_angle_1_deg | 8.109 |
r_scangle_it | 7.249 |
r_scangle_other | 7.249 |
r_mcangle_it | 5.693 |
r_mcangle_other | 5.692 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4982 |
Nucleic Acid Atoms | |
Solvent Atoms | 176 |
Heterogen Atoms | 100 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
PHASES | phasing |