De novo designed homo-trimeric amantadine-binding protein
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, SITTING DROP | 4 | 293 | 9% PEG6000, 0.1 M citric acid, pH 4.0 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.78 | 55.82 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 50.61 | α = 90 |
| b = 50.61 | β = 90 |
| c = 68.82 | γ = 120 |
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | IMAGE PLATE | RIGAKU | | 2017-12-09 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 298 | IMAGE PLATE | MAATEL IMAGINE | | 2018-06-12 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5417 | | |
| 2 | NUCLEAR REACTOR | ORNL High Flux Isotope Reactor BEAMLINE CG4D | 2.8-4.5 | ORNL High Flux Isotope Reactor | CG4D |
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 | 1.92 | 68.82 | 100 | 0.09 | | | | | | 23.2 | 17.8 | | 7655 | | | |
| 2 | 2.3 | 36.72 | 73.5 | 0.143 | | | | | | 8.7 | 4 | | 2639 | | | |
| 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 | 1.92 | 9.02 | | | | | | | | | | |
| 2 | 2.5 | 7.27 | | | | | | | | | | |
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 | R-Free | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.923 | 36.969 | | 1.38 | | 7655 | 770 | 99.87 | | 0.1777 | 0.1748 | 0.2039 | | |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.5 | 27.065 | | 23.7 | | 2639 | 261 | 75.34 | | 0.2801 | 0.2771 | 0.3179 | | |
| 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 | 14.512 |
| f_dihedral_angle_d | 14.512 |
| f_angle_d | 2.001 |
| f_angle_d | 2.001 |
| f_chiral_restr | 0.073 |
| f_chiral_restr | 0.073 |
| f_bond_d | 0.013 |
| f_bond_d | 0.013 |
| f_plane_restr | 0.01 |
| f_plane_restr | 0.01 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 596 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 41 |
| Heterogen Atoms | 12 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| LAUEGEN | data reduction |
| LSCALE | data scaling |
| PHASER | phasing |
