5LC0

Crystal structure of Zika virus NS2B-NS3 protease in complex with a boronate inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2911.5 M lithium sulfate monohydrate, 0.1 M sodium acetate trihydrate, pH 4.8.
Crystal Properties
Matthews coefficientSolvent content
3.4764.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.808α = 90
b = 125.808β = 90
c = 73.461γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.03320PETRA III, DESYP11

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
12.773.461000.07219.59.218733
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)
12.72.851000.7932.79.9

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 REPLACEMENTTHROUGHOUT2YOL2.762.91781090299.980.206650.203790.26332RANDOM93.519
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]
-50.14-50.14100.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.534
r_dihedral_angle_4_deg19.912
r_dihedral_angle_3_deg19.15
r_long_range_B_refined12.882
r_long_range_B_other12.881
r_mcangle_it9.393
r_mcangle_other9.392
r_scangle_other9.029
r_dihedral_angle_1_deg8.782
r_mcbond_it6.386
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.534
r_dihedral_angle_4_deg19.912
r_dihedral_angle_3_deg19.15
r_long_range_B_refined12.882
r_long_range_B_other12.881
r_mcangle_it9.393
r_mcangle_other9.392
r_scangle_other9.029
r_dihedral_angle_1_deg8.782
r_mcbond_it6.386
r_mcbond_other6.383
r_scbond_it6.088
r_scbond_other6.086
r_angle_refined_deg1.622
r_angle_other_deg1.134
r_chiral_restr0.14
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.003
r_bond_other_d0.002
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2892
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing