structure of HEX-1 from N. crassa crystallized in cellulo, diffracted at 100K and resolved using XDS
X-RAY DIFFRACTION
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1KHI | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | IN CELL | 300 | baculovirus infected and grown in Trichoplusia ni (High Five) cells in adhesion culture (MOI 1) | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.45 | 49.74 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.24 | α = 90 |
| b = 57.24 | β = 90 |
| c = 198.19 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 2 2 |
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 16M | 2019-11-26 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) | 0.980 | PETRA III, EMBL c/o DESY | P14 (MX2) |
Serial Crystallography
| Sample delivery method | ||
|---|---|---|
| Diffraction ID | Description | Sample Delivery Method |
| 1 | fixed target | |
| Fixed Target | ||||||
|---|---|---|---|---|---|---|
| Diffraction ID | Description | Sample Holding | Support Base | Motion control | Details | Sample Solvent |
| 1 | Micro mesh mount | |||||
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 | 1.85 | 33.03 | 99.8 | 0.999 | 35.15 | 4639 | 33344 | 31.25 | |||||||||||
| 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 | 1.85 | 1.916 | 0.939 | ||||||||||||||||
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-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.85 | 33.03 | 1.35 | 33344 | 2257 | 99.02 | 0.206 | 0.204 | 0.2332 | 0.2394 | 42.06 | ||||||
| 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 | 6.1181 |
| f_angle_d | 0.8646 |
| f_chiral_restr | 0.0663 |
| f_plane_restr | 0.0068 |
| f_bond_d | 0.0062 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1114 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 78 |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |














