7MMC

Crystal structure of HCV NS3/4A D168A protease in complex with NR01-115


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VOJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350 The cryogenic condition is 100 mM MES Buffer pH 6.5, 4% (W/V) Ammonium Sulfate, 20-26% PEG 3350, 15% Ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
3.0259.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.33α = 90
b = 58.919β = 90
c = 96.208γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442020-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.00124.0595.950.98215.2561731125.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.0012.0720.975

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5VOJ2.00124.051.351730286696.030.18870.18730.21430.59
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.3066
f_angle_d0.8311
f_chiral_restr0.0467
f_plane_restr0.006
f_bond_d0.0027
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1419
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms105

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
HKL-3000data scaling
Cootmodel building