X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7JSD | |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7 | 291 | HalA crystals were obtained by the hanging drop vapor diffusion method by combining equal volumes of protein solution (HalA (5 mg/ml), lysine (50 mM, pH 7), sodium succinate (20 mM, pH 7), sodium chloride (100 mM) and vanadium(IV) oxide sulfate hydrate (1 mM)) and reservoir solution (potassium phosphate monobasic (40 mM), 20% (w/v) PEG 8000, 15% (v/v) glycerol) |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.51 | 51.02 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 147.324 | α = 90 |
| b = 147.324 | β = 90 |
| c = 286.831 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | H 3 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 90 | PIXEL | DECTRIS PILATUS3 S 6M | 2022-05-06 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ALS BEAMLINE 8.3.1 | 1.11583 | ALS | 8.3.1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.67 | 116.57 | 100 | 0.2876 | 0.2917 | 0.04875 | 0.999 | 13.01 | 35.58 | 269701 | |||||||||
| 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 | 1.67 | 1.73 | 100 | 4.69 | 4.767 | 0.8489 | 0.59 | 1.49 | 30.85 | ||||||||||
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-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1.67 | 95.61 | 1.96 | 269463 | 13540 | 100 | 0.1906 | 0.1851 | 0.1864 | 0.2131 | 0.2133 | ||||||
| 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 | 14.271 |
| f_angle_d | 0.64 |
| f_chiral_restr | 0.043 |
| f_plane_restr | 0.006 |
| f_bond_d | 0.004 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 15413 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 1136 |
| Heterogen Atoms | 168 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
