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X-ray structure of the Grapevine Fanleaf virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y26 PDB ENTRY 2Y26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 CRYSTALS OF GFLV-F13 WERE GROWN AT 293K BY VAPOR DIFFUSION (1 MICROLITER SITTING DROPS) WITH A VIRUS SOLUTION AT 2.2 MG/ML AND A RESERVOIR CONTAINING 4% (M/V) PEG 3350, 0.1 M HEPES NA PH 7.5 AND 0.2% (M/V) AGAROSE.
Crystal Properties Matthews coefficient Solvent content 5.27 76.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 279.4 α = 102.4 b = 279.6 β = 116.4 c = 293.3 γ = 108.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2009-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 135.426 88.1 0.1 9.2 2 1214112 36.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.08 71.7 0.36 2.5 2
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 2Y26 3 135.426 1214112 60925 88.26 0.1911 0.1902 0.1865 0.2073 0.2033 36.27
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] 0.628 -0.5939 2.5481 -5.1409 5.1099 5.5261
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.539 f_angle_d 1.195 f_chiral_restr 0.077 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 79020 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose AMoRE model building PHENIX refinement XDS data reduction XSCALE data scaling AMoRE phasing