Room temperature serial crystal structure of Glutaminase C in complex with inhibitor BPTES
Serial Crystallography (SX)
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 5WJ6 | PDB entry 5WJ6 |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | VAPOR DIFFUSION, HANGING DROP | | 298 | 1.0 M lithium chloride, 10% PEG6000, 0.1 M Tris, pH 8.5 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.62 | 53.09 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 50 | α = 90 |
| b = 138 | β = 90.001 |
| c = 178 | 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 | 298 | PIXEL | DECTRIS EIGER R 1M | | 2020-06-10 | M | SINGLE WAVELENGTH |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | SYNCHROTRON | CHESS BEAMLINE G3 | 1.127 | CHESS | G3 |
Serial Crystallography
| Sample delivery method |
|---|
| Diffraction ID | Description | Sample Delivery Method |
|---|
| 1 | | fixed target |
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 | 3 | 20.33 | 97.6 | 0.97 | 5.4 | 19.8 | | 47136 | | | 79.49 |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 3 | 3.07 | 98.6 | | 0.45 | | | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 5WJ6 | 3 | 20.33 | 1.34 | 46924 | 2000 | 97.28 | 0.2108 | 0.2074 | 0.21 | 0.2861 | 0.29 | 90.83 |
| 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 | 23.0232 |
| f_angle_d | 1.1893 |
| f_chiral_restr | 0.0582 |
| f_bond_d | 0.0091 |
| f_plane_restr | 0.0076 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 12293 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 4 |
| Heterogen Atoms | 70 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
