Crystal structure of human NQO1 by serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1DXQ | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | BATCH MODE | 8.5 | 293 | 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350, 20 um FAD |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.65 | 53.52 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 61.4 | α = 90 |
| b = 107.6 | β = 90 |
| c = 198.1 | γ = 90 |
| Symmetry |
|---|
| Space Group | P 21 21 21 |
|---|
Diffraction
| Diffraction Experiment |
|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
|---|
| 1 | 1 | x-ray | 298 | PIXEL | SLAC ePix10k | | 2021-05-27 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE MFX | 1.2848 | SLAC LCLS | MFX |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | Modular Droplet Injector | injection |
| Data Reduction |
|---|
| Diffraction ID | Frames Indexed | Crystal Hits | Frames Indexed | Latices Merged |
|---|
| 1 | | | | |
| Injection |
|---|
| Diffraction ID | Description | Flow Rate | Injector Diameter | Injection Power | Injector Nozzle | Filter Size | Carrier Solvent |
|---|
| 1 | Modular Droplet Injector | 5 (µl/min) | undefined (µm) | | | | Crystals in mother liquor encapsulated into oil droplets |
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 | 2.7 | 24 | 100 | 0.9668 | 1.9 | 46 | | 36928 | | | |
| 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 | 2.7 | 2.8 | 100 | | 0.458 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B |
|---|
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1DXQ | 2.7 | 23.922 | 36835 | 1822 | 99.724 | 0.227 | 0.225 | 0.23 | 0.2687 | 0.27 | 0.1 | 45.992 |
| 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] |
|---|
| 0.363 | | | 0.054 | | -0.417 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 16.632 |
| r_dihedral_angle_6_deg | 14.859 |
| r_dihedral_angle_2_deg | 8.131 |
| r_lrange_it | 7.232 |
| r_lrange_other | 7.232 |
| r_dihedral_angle_1_deg | 6.698 |
| r_scangle_it | 4.699 |
| r_scangle_other | 4.699 |
| r_mcangle_it | 4.172 |
| r_mcangle_other | 4.172 |
| RMS Deviations |
|---|
| Key | Refinement Restraint Deviation |
|---|
| r_dihedral_angle_3_deg | 16.632 |
| r_dihedral_angle_6_deg | 14.859 |
| r_dihedral_angle_2_deg | 8.131 |
| r_lrange_it | 7.232 |
| r_lrange_other | 7.232 |
| r_dihedral_angle_1_deg | 6.698 |
| r_scangle_it | 4.699 |
| r_scangle_other | 4.699 |
| r_mcangle_it | 4.172 |
| r_mcangle_other | 4.172 |
| r_scbond_it | 2.714 |
| r_scbond_other | 2.714 |
| r_mcbond_it | 2.491 |
| r_mcbond_other | 2.49 |
| r_angle_refined_deg | 1.162 |
| r_angle_other_deg | 0.381 |
| r_dihedral_angle_other_2_deg | 0.324 |
| r_symmetry_nbd_refined | 0.279 |
| r_nbd_other | 0.274 |
| r_symmetry_xyhbond_nbd_refined | 0.242 |
| r_nbd_refined | 0.211 |
| r_symmetry_nbd_other | 0.199 |
| r_xyhbond_nbd_refined | 0.186 |
| r_nbtor_refined | 0.184 |
| r_symmetry_nbtor_other | 0.081 |
| r_chiral_restr | 0.05 |
| r_bond_refined_d | 0.005 |
| r_gen_planes_refined | 0.004 |
| r_gen_planes_other | 0.002 |
| r_bond_other_d | 0.001 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 8646 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 163 |
| Heterogen Atoms | 228 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| REFMAC | refinement |
| CrystFEL | data reduction |
| Aimless | data scaling |
| PHASER | phasing |