6DFU
Tryptophan--tRNA ligase from Haemophilus influenzae.
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.6 | 289 | 0.1 M potassium thiocyanate, 30% PEG MME 2000, 10 mM tryptophane |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.21 | 44.35 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 70.294 | α = 90 |
| b = 48.677 | β = 101.13 |
| c = 99.322 | 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 | 100 | CCD | ADSC QUANTUM 210r | 2017-07-13 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9792 | APS | 19-BM |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (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 | 2.05 | 50 | 99.9 | 0.122 | 0.141 | 0.071 | 8.9 | 3.8 | 42196 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.05 | 2.09 | 99.3 | 0.642 | 0.76 | 0.401 | 0.875 | 3.4 | |||||||||||
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 3N9I | 2.05 | 35.5 | 40090 | 2084 | 98.01 | 0.1897 | 0.1872 | 0.238 | RANDOM | 37.432 | ||||||
| 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] | |
| -1.21 | 0.28 | 0.23 | 0.81 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 38.854 |
| r_dihedral_angle_4_deg | 20.257 |
| r_dihedral_angle_3_deg | 16.164 |
| r_dihedral_angle_1_deg | 5.794 |
| r_angle_refined_deg | 1.558 |
| r_angle_other_deg | 0.984 |
| r_chiral_restr | 0.09 |
| r_bond_refined_d | 0.013 |
| r_gen_planes_refined | 0.007 |
| r_bond_other_d | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 5225 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 196 |
| Heterogen Atoms | 30 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-3000 | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | phasing |
