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Satellite Tobacco Mosaic Virus Refined to 1.4 A Resolution using non-crystallographic symmetry 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 VAPOR DIFFUSION, SITTING DROP 6.5 296 crystals grown from 15% ammonium sulfate on earth with a reservoir of 15% ammonium sulfate over 14 days., pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.69 α = 90 b = 190.3 β = 90 c = 201.69 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 100 CCD ADSC QUANTUM 315 2003-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.06 ALS 8.2.2
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 1.4 48.35 95.4 0.1 11.6 7.23 643001 613720 26.95
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 1.4 1.45 67.3 0.354 2.9 2.17 43070
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1A34 1.45 48.35 570721 570721 28359 98.55 0.21817 0.21817 0.21652 0.24973 0.2821 RANDOM 45.601
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] -0.74 0.93 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.548 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 12.822 r_scangle_it 8.388 r_dihedral_angle_1_deg 6.901 r_scangle_other 6.189 r_scbond_other 5.7 r_scbond_it 5.504 r_mcangle_it 3.069 r_rigid_bond_restr 2.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.548 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 12.822 r_scangle_it 8.388 r_dihedral_angle_1_deg 6.901 r_scangle_other 6.189 r_scbond_other 5.7 r_scbond_it 5.504 r_mcangle_it 3.069 r_rigid_bond_restr 2.443 r_mcangle_other 2.039 r_mcbond_it 1.956 r_mcbond_other 1.811 r_angle_refined_deg 1.25 r_angle_other_deg 0.786 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.214 r_symmetry_vdw_other 0.21 r_metal_ion_refined 0.205 r_xyhbond_nbd_refined 0.202 r_symmetry_metal_ion_refined 0.201 r_nbd_other 0.197 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.178 r_xyhbond_nbd_other 0.124 r_symmetry_hbond_other 0.12 r_nbtor_other 0.087 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.002 r_metal_ion_other r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16770 Nucleic Acid Atoms 6720 Solvent Atoms 4276 Heterogen Atoms 125
Software Software Software Name Purpose ADSC data collection Coot model building REFMAC refinement d*TREK data reduction d*TREK data scaling CNS phasing