6KR3
Crystal structure of Dengue virus nonstructural protein NS5 (form 2)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | EVAPORATION | 6.1 | 289 | PEG3350 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
3.54 | 65.3 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 178.845 | α = 90 |
b = 209.975 | β = 90 |
c = 157.873 | γ = 90 |
Symmetry | |
---|---|
Space Group | C 2 2 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS PILATUS 6M | 2016-09-09 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL18U1 | 0.9788 | SSRF | BL18U1 |
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 | 2.93 | 60 | 99.9 | 0.138 | 0.153 | 0.064 | 6.1 | 5.6 | 63847 | 64.31 |
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 | 2.93 | 3.03 | 100 | 0.55 | 0.609 | 0.257 | 0.832 | 5.5 |
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 | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 4K6M, 4V0Q | 2.931 | 49.812 | 1.35 | 63805 | 3164 | 99.87 | 0.235 | 0.2333 | 0.2681 | 60.351 |
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 | 22.197 |
f_angle_d | 1.234 |
f_chiral_restr | 0.065 |
f_bond_d | 0.012 |
f_plane_restr | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 12757 |
Nucleic Acid Atoms | |
Solvent Atoms | 47 |
Heterogen Atoms | 153 |
Software
Software | |
---|---|
Software Name | Purpose |
HKL-2000 | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
PHASER | phasing |