Spitrobot-2 advances time-resolvedcryo-trapping crystallography to under 25 ms: Human insulin, pH 4.5 (5 s soaking)
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1B18 | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | BATCH MODE | 9 | 293 | 1.0 M sodium/potassium phosphate, pH 9.0 & crystal soaking in pH 4.5 for 5 s |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.42 | 63.99 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 78.131 | α = 90 |
| b = 78.131 | β = 90 |
| c = 78.131 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 21 3 |
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 EIGER X 4M | 2025-02-08 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.9677 | ESRF | MASSIF-3 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.293 | 39.065 | 91.4 | 0.992 | 6.5 | 5.58 | 16218 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.293 | 1.387 | 0.319 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | 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) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.3 | 39.1 | 15412 | 805 | 81.47 | 0.17674 | 0.17586 | 0.1844 | 0.1937 | 0.1998 | RANDOM | 15.023 | |||||
| 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 |
| r_dihedral_angle_3_deg | 11.611 |
| r_long_range_B_other | 7.605 |
| r_long_range_B_refined | 7.338 |
| r_dihedral_angle_1_deg | 6.236 |
| r_scangle_other | 5.374 |
| r_mcangle_other | 4.074 |
| r_mcangle_it | 4.034 |
| r_scbond_it | 3.328 |
| r_scbond_other | 3.304 |
| r_mcbond_it | 2.472 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 405 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 49 |
| Heterogen Atoms | 5 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| autoPROC | data reduction |
| Aimless | data scaling |
| autoPROC | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
