2FYQ
Crystal Structure of the Norwalk Virus Protease
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 5.5 | 298 | 0.1M lithium sulfate, 0.1M bis-tris, 0.1M EDTA, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.50 | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.87 | 57.14 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 121.833 | α = 90 |
| b = 121.833 | β = 90 |
| c = 51.369 | 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 | 93 | CCD | ADSC QUANTUM 4 | M | SINGLE WAVELENGTH | |||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.5 | 31.5 | 99.1 | 36055 | |||||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1.5 | 1.55 | 0.457 | 4.1 | ||||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Work | R-Free | Mean Isotropic B | |||||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.5 | 105.41 | 36046 | 36046 | 1800 | 99 | 0.185 | 0.211 | 17.31 | |||||||||
| 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] | |
| -0.06 | -0.03 | -0.06 | 0.09 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 37.522 |
| r_dihedral_angle_4_deg | 17.037 |
| r_dihedral_angle_3_deg | 11.219 |
| r_dihedral_angle_1_deg | 6.485 |
| r_sphericity_free | 3.076 |
| r_scangle_it | 2.794 |
| r_sphericity_bonded | 2.148 |
| r_scbond_it | 2.116 |
| r_rigid_bond_restr | 1.694 |
| r_mcangle_it | 1.494 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 1271 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 293 |
| Heterogen Atoms | 7 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| d*TREK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
