6GP9
Structural studies of hepatitis C virus non-structural protein-5b of genotype 4a
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1C2P |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.4 | 292 | 100 mM sodium citrate pH 5.4, 25-30% (v/v) PEG 550 MME |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.08 | 40.86 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 63.29 | α = 90 |
b = 87.05 | β = 90 |
c = 96.72 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 21 21 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 PILATUS3 2M | 2015-02-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE MASSIF-3 | 0.96500 | ESRF | MASSIF-3 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 3.1 | 100 | 99.7 | 0.138 | 0.995 | 9.23 | 3.9 | 10145 | 77.2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.1 | 3.18 | 100 | 0.8 | 0.713 | 1.74 | 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 | 1C2P | 3.1 | 64.7 | 9635 | 509 | 99.71 | 0.20462 | 0.20183 | 0.25735 | RANDOM | 70 |
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] | |
-6.75 | 2.5 | 4.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.264 |
r_dihedral_angle_4_deg | 22.612 |
r_dihedral_angle_3_deg | 18.379 |
r_long_range_B_refined | 13.688 |
r_mcangle_it | 7.198 |
r_dihedral_angle_1_deg | 5.844 |
r_scbond_it | 5.536 |
r_mcbond_it | 4.544 |
r_angle_refined_deg | 1.619 |
r_chiral_restr | 0.116 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 4324 |
Nucleic Acid Atoms | |
Solvent Atoms | 16 |
Heterogen Atoms |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
MOLREP | phasing |