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DESMODIUM YELLOW MOTTLE TYMOVIRUS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Turnip yellow mosaic virus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP 4.8 295 2 M SODIUM FORMATE, 0.1 M SODIUM ACETATE, POTASSIUM PHOSPHATE BUFFER, pH 4.8, VAPOR DIFFUSION, BOTH SITTING DROP AND HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.78 67.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 348.546 α = 90 b = 348.546 β = 90 c = 348.546 γ = 90
Symmetry Space Group P 42 3 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 295 IMAGE PLATE MARRESEARCH 1996-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 2.7 40 68.7 0.107 7.3 3.2 178705 178705 23.7
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) 2.7 2.8 82.7 0.453 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT TURNIP YELLOW MOSAIC VIRUS 2.7 40 1.5 3 178705 134454 13357 68.7 0.206 0.152 0.151 0.1666 0.159 0.1734 RANDOM 33.3
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d_na 39.3 x_scangle_it 23.41 x_dihedral_angle_d 20.3 x_dihedral_angle_d_prot 20.3 x_scbond_it 13.71 x_mcangle_it 5.86 x_mcbond_it 3.61 x_improper_angle_d_na 2.93 x_angle_deg_na 2.38 x_angle_deg 1.9
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d_na 39.3 x_scangle_it 23.41 x_dihedral_angle_d 20.3 x_dihedral_angle_d_prot 20.3 x_scbond_it 13.71 x_mcangle_it 5.86 x_mcbond_it 3.61 x_improper_angle_d_na 2.93 x_angle_deg_na 2.38 x_angle_deg 1.9 x_angle_deg_prot 1.9 x_improper_angle_d 1.32 x_improper_angle_d_prot 1.32 x_bond_d_na 0.015 x_bond_d 0.01 x_bond_d_prot 0.01 x_angle_d x_angle_d_na x_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4203 Nucleic Acid Atoms 182 Solvent Atoms 285 Heterogen Atoms
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing