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Crystallographic structure of the cubic crystal form of STMV (77.9 degree rotation) grown from NaCl
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OQ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 279 Crystals were grown by sitting drop vapor diffusion in Cryschem plates using 0.6 ml reservoirs. The drops were composed of equal amounts of a 5 mg/ml stock virus solution buffered at pH6.5 with 0.1 M phosphate, and the reservoir solution which was 8% w/v NaCl buffered with 0.1 M phosphate at pH 6.0. Crystallization was carried out at 4 degrees C.
Crystal Properties Matthews coefficient Solvent content 2.54 51.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.65 α = 90 b = 234.65 β = 90 c = 234.65 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 CCD MAR CCD 165 mm 2002-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 2.9 100.5 96 0.17 0.15 0.97 7.2 7.8 87022 43.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 75 0.32 0.52 2.8 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 4OQ8 2.94 78.22 1.34 86916 4392 95.43 0.2187 0.2168 0.2074 0.2556 0.2421 58.43
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 f_dihedral_angle_d 13.6359 f_angle_d 0.7153 f_chiral_restr 0.0616 f_plane_restr 0.012 f_bond_d 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22546 Nucleic Acid Atoms 2926 Solvent Atoms 915 Heterogen Atoms 53
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction d*TREK data reduction d*TREK data scaling PHASER phasing