2VBC

Crystal structure of the NS3 protease-helicase from Dengue virus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FOMPDB ENTRIES 2FOM AND 2BMF
experimental modelPDB 2BMFPDB ENTRIES 2FOM AND 2BMF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.3850.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.866α = 90
b = 88.242β = 94.21
c = 76.676γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
13.1588.399.80.14113.4122362
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)
13.153.399.80.682.13.4

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 ENTRIES 2FOM AND 2BMF3.15201158358399.80.2060.2020.277RANDOM61.03
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]
0.190.130.03-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.085
r_dihedral_angle_3_deg18.328
r_dihedral_angle_4_deg15.252
r_dihedral_angle_1_deg5.129
r_angle_refined_deg1.088
r_scangle_it0.809
r_mcangle_it0.48
r_scbond_it0.459
r_nbtor_refined0.307
r_mcbond_it0.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.085
r_dihedral_angle_3_deg18.328
r_dihedral_angle_4_deg15.252
r_dihedral_angle_1_deg5.129
r_angle_refined_deg1.088
r_scangle_it0.809
r_mcangle_it0.48
r_scbond_it0.459
r_nbtor_refined0.307
r_mcbond_it0.26
r_nbd_refined0.206
r_symmetry_vdw_refined0.15
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.13
r_chiral_restr0.072
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4834
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing