6XNF
GCN4-p1 Peptide Trimer with Tetrafluoroiodophenylalanine residue at position 16 (TFI-F16)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | Crystallization drops were prepared by mixing 2 uL of stock peptide solution with 2 uL of mother liquor and allowed to equilibrate at 298 K over a well containing 500 uL of mother liquor. The stock peptide solution (total concentration 1.5 mM) was prepared by mixing 2:1 ratios of the A16 peptide with TFI-F16 in 10 mM potassium phosphate, 100 mM potassium chloride pH 7.0. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.18 | 43.54 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 59.65 | α = 90 |
b = 35.19 | β = 100.647 |
c = 47.02 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 200K | 2017-08-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-003 | 1.5418 |
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 | 46.21 | 99.47 | 0.09809 | 0.1068 | 0.04159 | 0.996 | 11.38 | 6.5 | 43081 | 28.81 |
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 | 2.072 | 99.4 | 0.7578 | 0.3375 | 0.8326 | 0.766 | 2.69 | 6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1SWI | 2 | 46.21 | 1.34 | 12124 | 609 | 95.23 | 0.2002 | 0.1973 | 0.2537 | 39.45 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 2.9085 |
f_angle_d | 1.07 |
f_chiral_restr | 0.0579 |
f_bond_d | 0.0083 |
f_plane_restr | 0.0046 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 767 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
HKL-2000 | data reduction |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
PHENIX | phasing |