Joint X-ray/neutron structure of Salmonella typhimurium tryptophan synthase internal aldimine from microgravity-grown crystal
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) |
|---|
| Type | Source | Accession Code | Details |
|---|
|
experimental model | PDB | 1BKS | |
Crystallization
| Crystalization Experiments |
|---|
| ID | Method | pH | Temperature | Details |
|---|
| 1 | LIQUID DIFFUSION | 7.8 | 295 | 50 mM Bicine pH 7.8, 1 mM EDTA, 0.2 mM PLP, 2 mM spermine, and 6-8% PEG 8000 |
| Crystal Properties |
|---|
| Matthews coefficient | Solvent content |
|---|
| 2.68 | 54.08 |
Crystal Data
| Unit Cell |
|---|
| Length ( Å ) | Angle ( ˚ ) |
|---|
| a = 184.51 | α = 90 |
| b = 61.86 | β = 94.74 |
| c = 67.67 | γ = 90 |
| Symmetry |
|---|
| Space Group | C 1 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 | 289 | PIXEL | DECTRIS EIGER R 4M | | 2020-01-27 | M | SINGLE WAVELENGTH |
| 2 | 1 | neutron | 289 | IMAGE PLATE | LADI III | | 2021-07-10 | L | LAUE |
| Radiation Source |
|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
|---|
| 1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
| 2 | NUCLEAR REACTOR | ILL BEAMLINE LADI III | 2.85-3.8 | ILL | LADI III |
Data Collection
| Overall |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.8 | 91.91 | 93 | 0.052 | | | | | | 26.6 | 3 | | 65668 | | | |
| 2 | 2.1 | 52.36 | 70.1 | 0.182 | | | | | | 10.4 | 6.8 | | 30993 | | | |
| Highest Resolution Shell |
|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
|---|
| 1 | 1.8 | 1.86 | | 0.311 | | | | | | 2.4 | 2 | |
| 2 | 2.1 | 2.21 | | 0.41 | | | | | | 2 | 5.7 | |
Refinement
| Statistics |
|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | 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 | 1.8 | 29.44 | | | 70615 | 62584 | 3124 | 88.6 | | | 0.182 | 0.18 | 0.199 | 0.2 | RANDOM | 46.29 |
| NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.1 | 37.6 | | | 44653 | 26890 | 1341 | 60.2 | | | 0.224 | | 0.288 | | RANDOM | 46.29 |
| 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 |
|---|
| x_torsion_deg | 28.2 |
| x_torsion_deg | 28.2 |
| x_angle_deg | 1.1 |
| x_angle_deg | 1.1 |
| x_torsion_impr_deg | 0.8 |
| x_torsion_impr_deg | 0.8 |
| x_bond_d | 0.009 |
| x_bond_d | 0.009 |
| Non-Hydrogen Atoms Used in Refinement |
|---|
| Non-Hydrogen Atoms | Number |
|---|
| Protein Atoms | 4939 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 256 |
| Heterogen Atoms | 1 |
Software
| Software |
|---|
| Software Name | Purpose |
|---|
| nCNS | refinement |
| CrysalisPro | data reduction |
| CrysalisPro | data scaling |
| LAUEGEN | data reduction |
| LSCALE | data scaling |
