3MYZ
Protein induced photophysical changes to the amyloid indicator dye, thioflavin T
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1KPR | PDB ENTRY 1KPR |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.5 | 298 | 25% PEG 3350, 50mM diammonium tartrate, 5mM Thioflavin T, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.17 | 43.31 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 48.349 | ¦Á = 90 |
b = 28.467 | ¦Â = 91.42 |
c = 74.983 | ¦Ã = 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 | CCD | ADSC QUANTUM 315 | 2008-11-14 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 24-ID-E | 1.00 | APS | 24-ID-E |
2 | SYNCHROTRON | NSLS BEAMLINE X25 | 1.00 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | 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 | 1.6 | 50 | 98.3 | 0.082 | 0.082 | 8.89 | 1.9 | 38793 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1.6 | 1.83 | 88.3 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 1KPR | 1.6 | 29.27 | 20653 | 26034 | 1398 | 99.8 | 0.191 | 0.189 | 0.223 | RANDOM | 31.14 |
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] | |
0.07 | 0.05 | -0.04 | -0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.171 |
r_dihedral_angle_4_deg | 17.169 |
r_dihedral_angle_3_deg | 13.336 |
r_dihedral_angle_1_deg | 6.641 |
r_scangle_it | 3.174 |
r_mcangle_it | 2.889 |
r_scbond_it | 2.077 |
r_mcbond_it | 1.775 |
r_angle_refined_deg | 1.542 |
r_angle_other_deg | 1.12 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1628 |
Nucleic Acid Atoms | |
Solvent Atoms | 160 |
Heterogen Atoms | 83 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |