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Satellite Tobacco Mosaic Virus Refined at room temperature to 1.8 A Resolution using NCS Restraints
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A34 PDB entry 1A34
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 6.5 296 9 crystals were grown in microgravity aboard IML-I mission of the U.S. Space Shuttle over 12 days using 20% ammonium sulfate as precipitant, pH 6.50, LIQUID DIFFUSION, temperature 296K 2 VAPOR DIFFUSION, SITTING DROP 6.5 296 12 crystals grown from 8% ammonium sulfate on earth with a reservoir of 14-16% ammonium sulfate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.268 α = 90 b = 191.774 β = 90 c = 202.503 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 290 AREA DETECTOR SDMS 1992-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 1.82 87.04 89.46 0.091 8.2 271689 268316 24.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.82 1.919 75
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1A34 1.82 87.04 271689 268316 3984 89.5 0.124 0.123 0.1305 0.156 0.1606 RANDOM 41.09
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] 0.08 0.02 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 12.881 r_scangle_it 9.743 r_dihedral_angle_1_deg 6.533 r_scbond_it 6.089 r_mcangle_it 4.739 r_mcbond_it 2.915 r_mcbond_other 1.282 r_angle_refined_deg 1.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.892 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 12.881 r_scangle_it 9.743 r_dihedral_angle_1_deg 6.533 r_scbond_it 6.089 r_mcangle_it 4.739 r_mcbond_it 2.915 r_mcbond_other 1.282 r_angle_refined_deg 1.263 r_angle_other_deg 0.654 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16770 Nucleic Acid Atoms 6720 Solvent Atoms 3381 Heterogen Atoms 23
Software Software Software Name Purpose SDMS data collection REFMAC refinement SDMS data reduction SDMS data scaling