2FZ2

Structure of Turnip Yellow Mosaic Virus at 100 K


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.42981.0-1.7 M NH4PO4, 0.1 M MES buffer, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.1570.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 511.53α = 90
b = 511.53β = 90
c = 303.76γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Vertical and toroidal focusing mirror1998-12-11MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 4Vertical and toroidal focusing mirror1999-11-20MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2
2SYNCHROTRONALS BEAMLINE 5.0.21.25ALS5.0.2

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
1,22.6159.1235.30.1067.493.224765022584534
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.612.650.5-0.411172

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1AUY2.959.1222464122158391085742.80.3270.2770.2760.289RANDOM29.3
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]
-5.626.21-5.6211.24
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d29.9
c_scangle_it9.71
c_scbond_it6.88
c_mcangle_it6.35
c_mcbond_it4.08
c_angle_deg1.8
c_improper_angle_d0.95
c_bond_d0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4065
Nucleic Acid Atoms57
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing