3RNV

Structure of the autocatalytic cysteine protease domain of potyvirus helper-component proteinase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.42771M (NH4)2SO4, 4%(w/v) PEG3350, 0.1M Bis-Tris, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2244.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.806α = 90
b = 98.806β = 90
c = 65.747γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9796SSRFBL17U

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
122098.60.07348.713.111250
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)
22.0398.70.5284.110.6552

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2191061252698.690.247510.246290.27411RANDOM56.32
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]
-0.1-0.10.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.349
r_dihedral_angle_3_deg14.678
r_dihedral_angle_4_deg11.057
r_dihedral_angle_1_deg5.01
r_scangle_it2.521
r_scbond_it1.455
r_angle_refined_deg1.051
r_mcangle_it1.043
r_mcbond_it0.549
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.349
r_dihedral_angle_3_deg14.678
r_dihedral_angle_4_deg11.057
r_dihedral_angle_1_deg5.01
r_scangle_it2.521
r_scbond_it1.455
r_angle_refined_deg1.051
r_mcangle_it1.043
r_mcbond_it0.549
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms991
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms

Software

Software
Software NamePurpose
SHARPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling