4E7A

Crystal structure of a product state assembly of HCV NS5B genotype 2a JFH-1 isolate with beta hairpin deletion bound to primer-template RNA with a 2',3'-ddC


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E76PDB ENTRY 4E76

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62894.37 mg/mL NS5B in 20 mM Tris, pH 8, 200 mM sodium chloride, 20% glycerol, 2 mM TCEP, 200 mM imidazole against 30% PEG3350, 0.1 M Bis-Tris propane, pH 6.0, 200 mM ammonium acetate soaked overnight in precipitant supplemented with 15% ethylene glycol as cryoprotectant and 0.2 mM CUAGGC(DOC), crystal tracking ID 228018H11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.9568.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.73α = 90
b = 142.73β = 90
c = 91.5γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
135099.50.09916.765.32139521289-359.238
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.0899.60.7452.27

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4E7635021288109399.50.1970.1940.241RANDOM55.3872
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]
2.51.252.5-3.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.612
r_dihedral_angle_3_deg17.484
r_dihedral_angle_4_deg13.772
r_dihedral_angle_1_deg6.125
r_angle_refined_deg1.34
r_angle_other_deg0.899
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.612
r_dihedral_angle_3_deg17.484
r_dihedral_angle_4_deg13.772
r_dihedral_angle_1_deg6.125
r_angle_refined_deg1.34
r_angle_other_deg0.899
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4038
Nucleic Acid Atoms197
Solvent Atoms18
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction