Human DJ-1, 10 sec mixing with methylglyoxal, pink beam time-resolved serial crystallography, CrystFEL processed
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | Other | | Unpublished DJ-1 structure from X-ray source |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 7.5 | 293 | 100 mM HEPES, 200 mM NaCl, 15% (w/v) PEG 3350 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 3.15 | 60.89 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 76.03 | α = 90 |
| b = 76.03 | β = 90 |
| c = 76.14 | γ = 120 |
| Symmetry |
|---|
| Space Group | P 31 2 1 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 293 | CCD | RAYONIX MX340-HS | | 2022-11-13 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | APS BEAMLINE 14-ID-B | 1.240-1.016 | APS | 14-ID-B |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | concentric flow microfluidic mixer | injection |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | 1477 | 1518 | 1477 | |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.77 | 65.84 | 99.01 | 0.99 | 0.101 | 4.68 | 95.32 | | 24998 | | | 27.55 |
| 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 | 1.77 | 1.8 | 98.7 | | 0.05 | 0.31 | 90.5 | |
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 | FOURIER SYNTHESIS | FREE R-VALUE | 1.97 | 32.96 | 1.34 | 18236 | 902 | 99.06 | 0.15 | 0.1485 | 0.1487 | 0.1772 | 0.175 | 34.46 |
| 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 | 13.4792 |
| f_angle_d | 0.7415 |
| f_chiral_restr | 0.0488 |
| f_plane_restr | 0.006 |
| f_bond_d | 0.0059 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 1383 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 124 |
| Heterogen Atoms | 5 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| PHENIX | refinement |
| Precognition | data reduction |
| CrystFEL | data scaling |
| PHENIX | phasing |
