7KJJ
Reconstructed ancestor of HIUases and Transthyretins
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 291.15 | Condition 1: 2 M lithium sulfate, 5% (v/v) 2-propanol, 0.1 M magnesium sulfate, 0.2 M sodium acetate pH 4.5 Condition 2: 30% (w/v) PEG 1500, 20% (w/v) PEG 400, 0.1 M Hepes pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.24 | 61.99 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 92.43 | α = 90 |
b = 92.43 | β = 90 |
c = 87.78 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS3 2M | 2018-10-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | LNLS BEAMLINE W01B-MX2 | 1.459 | LNLS | W01B-MX2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 1.55 | 41.34 | 99.9 | 0.037 | 0.99 | 26.3 | 6.3 | 55503 | 20.27 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.55 | 1.59 | 99.2 | 0.703 | 0.868 | 2.9 | 5.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | FREE R-VALUE | 1.55 | 40.89 | 1.35 | 55477 | 2666 | 99.89 | 0.1727 | 0.1721 | 0.1846 | 30.24 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.5707 |
f_angle_d | 1.4746 |
f_chiral_restr | 0.0991 |
f_bond_d | 0.0157 |
f_plane_restr | 0.0103 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1792 |
Nucleic Acid Atoms | |
Solvent Atoms | 178 |
Heterogen Atoms | 52 |
Software
Software | |
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Software Name | Purpose |
MxCuBE | data collection |
XDS | data reduction |
Coot | model building |
PHENIX | phasing |
PHENIX | refinement |
XDS | data scaling |