6MO1

Structure of dengue virus protease with an allosteric Inhibitor that blocks replication


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29535% PEG 200, 100 mM MES, pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.550.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.325α = 90
b = 109.325β = 90
c = 76.255γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2018-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

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
12.7501000.44511.489.314737
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)
12.72.899.82.4091.297.8

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 REPLACEMENTTHROUGHOUT2FOM347.381034850199.940.241210.237820.31201RANDOM58.881
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]
-3.62-1.81-3.6211.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.348
r_dihedral_angle_3_deg29.381
r_dihedral_angle_4_deg20.683
r_long_range_B_refined12.905
r_long_range_B_other12.905
r_mcangle_it11.85
r_mcangle_other11.849
r_scangle_other11.497
r_mcbond_it8.805
r_mcbond_other8.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.348
r_dihedral_angle_3_deg29.381
r_dihedral_angle_4_deg20.683
r_long_range_B_refined12.905
r_long_range_B_other12.905
r_mcangle_it11.85
r_mcangle_other11.849
r_scangle_other11.497
r_mcbond_it8.805
r_mcbond_other8.805
r_scbond_it8.703
r_scbond_other8.7
r_rigid_bond_restr7.096
r_dihedral_angle_1_deg4.079
r_angle_other_deg1.71
r_angle_refined_deg1.488
r_chiral_restr0.074
r_bond_other_d0.018
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.005
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_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2512
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing