☰ Navigation Tabs
Structure Determination of A223, a turret protein in Sulfolobus turreted icosahedral virus, using an iterative hybrid approach
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3J31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 Crystals of A223-L208M were grown by hanging drop vapour diffusion using 2 micro-L of the protein solution and 2 micro-L in 0.1 M tri-sodium citrate dihydrate pH 5.6 and 35% t-butanol.
Crystal Properties Matthews coefficient Solvent content 2.62 53.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.995 α = 90 b = 56.995 β = 90 c = 272.807 γ = 120
Symmetry Space Group P 31 2 1
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 MARRESEARCH Mirror: Rh coated flat bent M0, toroidal focusing post-monochromator M1 2009-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.82653 SSRL BL9-2
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 1.82 50 99.7 0.043 16.9 5.4 47436
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 1.82 1.89 99.8 0.53 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3J31 1.83 20.85 44222 2466 99.8 0.16534 0.16364 0.1682 0.19542 0.192 RANDOM 35.73
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] 17.19 17.19 -34.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.511 r_dihedral_angle_4_deg 34.118 r_dihedral_angle_3_deg 13.219 r_sphericity_free 8.878 r_dihedral_angle_1_deg 6.899 r_sphericity_bonded 3.71 r_rigid_bond_restr 3.706 r_angle_refined_deg 1.426 r_angle_other_deg 0.721 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.511 r_dihedral_angle_4_deg 34.118 r_dihedral_angle_3_deg 13.219 r_sphericity_free 8.878 r_dihedral_angle_1_deg 6.899 r_sphericity_bonded 3.71 r_rigid_bond_restr 3.706 r_angle_refined_deg 1.426 r_angle_other_deg 0.721 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2967 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing