3LKW

Crystal Structure of Dengue Virus 1 NS2B/NS3 protease active site mutant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52930.1M Hepes pH 7.5, 12% PEG 3350, 0.005M each NiCl2, CdCl2, MgCl2, CoCl2, 0.1M Potassium sodium tartrate tetrahydrate, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.868α = 90
b = 60.893β = 90
c = 160.616γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
11.995098.10.07136.819014
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)
1.992.0479.60.4843.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2501901097397.80.2070.2050.249RANDOM40.25
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]
0.08-0.360.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.483
r_dihedral_angle_3_deg15.476
r_dihedral_angle_4_deg12.612
r_dihedral_angle_1_deg7.636
r_scangle_it6.211
r_scbond_it3.892
r_mcangle_it2.609
r_angle_refined_deg1.931
r_mcbond_it1.439
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.483
r_dihedral_angle_3_deg15.476
r_dihedral_angle_4_deg12.612
r_dihedral_angle_1_deg7.636
r_scangle_it6.211
r_scbond_it3.892
r_mcangle_it2.609
r_angle_refined_deg1.931
r_mcbond_it1.439
r_chiral_restr0.144
r_bond_refined_d0.024
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1593
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling