5EZS

Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited by E64d


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.6290JCSG+ Condition #8 (0.2 M Ammonium formate, 20% PEG 3350)
Crystal Properties
Matthews coefficientSolvent content
2.3243.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.89α = 90
b = 63.63β = 90
c = 86.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDBruker Platinum 1352015-03-06MSINGLE 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
12.1660.8999.20.059114.167.31860516
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)
12.162.2696.20.26554.914.04

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 REPLACEMENTTHROUGHOUT2HWK2.1651.311764990699.210.191610.189760.22702RANDOM17.415
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.674
r_dihedral_angle_4_deg14.477
r_dihedral_angle_3_deg12.673
r_dihedral_angle_1_deg6.293
r_angle_other_deg3.703
r_long_range_B_refined3.383
r_long_range_B_other3.213
r_angle_refined_deg1.383
r_mcangle_it1.254
r_mcangle_other1.254
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.674
r_dihedral_angle_4_deg14.477
r_dihedral_angle_3_deg12.673
r_dihedral_angle_1_deg6.293
r_angle_other_deg3.703
r_long_range_B_refined3.383
r_long_range_B_other3.213
r_angle_refined_deg1.383
r_mcangle_it1.254
r_mcangle_other1.254
r_scangle_other1.103
r_mcbond_it0.687
r_mcbond_other0.686
r_scbond_it0.625
r_scbond_other0.624
r_chiral_restr0.099
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_gen_planes_other0.005
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 Atoms2551
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing