5K1J
Human TTR altered by a rhenium tris-carbonyl Pyta-C8 derivative
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4PME |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 293 | protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5 precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0 cryosoak: 40% SM2 (12.5 % ethylene glycol, 12.5 % glycerol, 12.5 % 1,2-propanediol, 25 % DMSO and 37.5% 1,4-dioxane) 50% PEG 8K and 0.2 milli-M of rhenium tris-carbonyl Pyta-C8 derivative. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.29 | 46.24 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 42.82 | α = 90 |
b = 83.1 | β = 90 |
c = 65.34 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 EIGER X 16M | mirrors | 2016-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 1.175919 | SOLEIL | PROXIMA 2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (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 | 1.69 | 50 | 99.1 | 0.033 | 0.028 | 1 | 22.92 | 3.45 | 49863 | -3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.69 | 1.74 | 92.4 | 0.631 | 2.22 | 2.88 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4PME | 1.69 | 41.55 | 25309 | 1332 | 99.59 | 0.17391 | 0.17134 | 0.22199 | RANDOM | 30.101 |
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] | |
-1.07 | -0.14 | 1.21 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.315 |
r_dihedral_angle_4_deg | 20.511 |
r_dihedral_angle_3_deg | 15.686 |
r_long_range_B_refined | 10.625 |
r_long_range_B_other | 10.623 |
r_scangle_other | 7.589 |
r_dihedral_angle_1_deg | 6.537 |
r_scbond_it | 4.957 |
r_scbond_other | 4.955 |
r_mcangle_it | 4.578 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1792 |
Nucleic Acid Atoms | |
Solvent Atoms | 167 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |