A DNA-stabilized atomically precise silver nanorod with emission at 960 nm
X-RAY DIFFRACTION
Serial Crystallography (SX)
Serial Crystallography (SX)
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293 | 50 mM MOPS, 10 mM spermine, 10 mM KNO3, 10% MPD |
| 2 | VAPOR DIFFUSION, HANGING DROP | 7 | 293 | 50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Ca(NO3), 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol. |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 27.215 | α = 90 |
| b = 53.171 | β = 103.67 |
| c = 27.215 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 1 |
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 PILATUS 6M | 2024-10-12 | M | SINGLE WAVELENGTH | ||||||
| 2 | 2 | x-ray | 100 | PIXEL | DECTRIS EIGER2 S 16M | 2024-10-20 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PHOTON FACTORY BEAMLINE BL-5A | 1.9 | Photon Factory | BL-5A |
| 2 | SYNCHROTRON | MAX IV BEAMLINE BioMAX | 0.6199 | MAX IV | BioMAX |
Serial Crystallography
| Sample delivery method | ||
|---|---|---|
| Diffraction ID | Description | Sample Delivery Method |
| 1 | fixed target | |
| 2 | fixed target | |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | ||||||
| 2 | 1.3 | 26.4 | 97.1 | 0.111 | 0.13 | 0.993 | 7.25 | 3.6 | 35689 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 2 | 1.3 | 1.33 | 0.319 | 0.376 | 0.899 | ||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 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 (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | AB INITIO PHASING | FREE R-VALUE | 1.3 | 16.82 | 1.98 | 35654 | 3521 | 97.16 | 0.1632 | 0.1631 | 0.1557 | 0.1642 | 0.1565 | ||||||
| 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 | 28.714 |
| f_angle_d | 1.21 |
| f_chiral_restr | 0.097 |
| f_plane_restr | 0.018 |
| f_bond_d | 0.009 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | |
| Nucleic Acid Atoms | 646 |
| Solvent Atoms | 39 |
| Heterogen Atoms | 30 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| XSCALE | data scaling |
| Sir2014 | phasing |
| AutoSol | phasing |
| XDS | data reduction |
