Neutron and X-ray joint structure of WT-TTR in complex with piceatannol
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 8W43 | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | | 293 | Disodium malonate, 0.1M NaOAc pH 4.6 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 1.75 | 29.8 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 43.67 | α = 90 |
| b = 85.014 | β = 90 |
| c = 65.353 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 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 | 293 | PIXEL | DECTRIS EIGER X 16M | | 2022-06-19 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 293 | DIFFRACTOMETER | iBIX | | 2022-05-13 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-17A | 0.98 | Photon Factory | BL-17A |
| 2 | SPALLATION SOURCE | J-PARC MLF BEAMLINE BL-03 | 2.8-5.7 | JPARC MLF | BL-03 |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.19 | 42.51 | 99.8 | | | 0.04 | 0.016 | 0.999 | | 23.8 | 6.3 | | 78555 | | | |
| 2 | 1.9 | 22.33 | 98.8 | | | 0.153 | 0.062 | 0.994 | | 14.9 | 6.97 | | 19613 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.19 | 1.23 | | | | 0.876 | 0.352 | 0.774 | | 2.3 | | |
| 2 | 1.9 | 1.97 | | | | 0.646 | 0.315 | 0.556 | | 2.7 | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.19 | 42.507 | | 1.36 | | 78550 | 3927 | 99.77 | | 0.1804 | 0.1793 | 0.18 | 0.2018 | 0.2 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.9 | 21.784 | | | | 19579 | 977 | 98.87 | | 0.1797 | 0.1783 | | 0.2064 | | | |
| 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 |
|---|
| Key | Refinement Restraint Deviation |
|---|
| f_dihedral_angle_d | 19.121 |
| f_dihedral_angle_d | 19.121 |
| f_angle_d | 0.917 |
| f_angle_d | 0.917 |
| f_chiral_restr | 0.096 |
| f_chiral_restr | 0.096 |
| f_bond_d | 0.029 |
| f_bond_d | 0.029 |
| f_plane_restr | 0.005 |
| f_plane_restr | 0.005 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1771 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 102 |
| Heterogen Atoms | 36 |
