5EZQ

Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural protein 2 (nsP2) Cysteine Protease


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HWK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5290JCSG+ Condition #15 (0.1 M Bicine pH 8.5, 20% PEG 6000)
Crystal Properties
Matthews coefficientSolvent content
2.1743.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.805α = 90
b = 63.72β = 90
c = 86.078γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDBRUKER SMART 60002015-01-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.6663.7299.60.040621.916.0140129
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)
11.661.7697.70.37513.242.95

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 REPLACEMENTTHROUGHOUT2hwk1.6651.2138017194199.330.202710.202290.21088RANDOM16.608
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]
-0.990.830.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.558
r_dihedral_angle_4_deg14.585
r_dihedral_angle_3_deg12.79
r_dihedral_angle_1_deg5.867
r_angle_other_deg3.651
r_long_range_B_refined3.431
r_long_range_B_other3.178
r_mcangle_it1.356
r_mcangle_other1.356
r_scangle_other1.202
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.558
r_dihedral_angle_4_deg14.585
r_dihedral_angle_3_deg12.79
r_dihedral_angle_1_deg5.867
r_angle_other_deg3.651
r_long_range_B_refined3.431
r_long_range_B_other3.178
r_mcangle_it1.356
r_mcangle_other1.356
r_scangle_other1.202
r_angle_refined_deg1.163
r_mcbond_it0.746
r_mcbond_other0.745
r_scbond_it0.678
r_scbond_other0.678
r_chiral_restr0.071
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d
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 Atoms2558
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing