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Crystal Structure of Reovirus T3D Attachment Protein Sigma1 head domain wild-type at 1.75 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KKE residues 293-455 of 1KKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 0.1 M sodium cacodylate, 0.2 M magnesium sulfate, 10-12% PEG 8000; protein concentration 13.6 mg/ml, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.927 α = 90 b = 51.381 β = 95.66 c = 108.87 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 2004-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.1 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 30 96.7 0.093 9.3 15.71 3.3 93625 90611 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 86.7 0.427 0.427 2.26 2.6 8020
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 residues 293-455 of 1KKE 1.75 30 93598 90462 9050 96.65 0.23222 0.22764 0.2263 0.27373 0.2706 RANDOM 15.731
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] -0.96 0.09 1.29 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 14.27 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 6.402 r_scangle_it 2.483 r_scbond_it 1.579 r_mcangle_it 1.378 r_angle_refined_deg 0.963 r_mcbond_it 0.842 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 14.27 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 6.402 r_scangle_it 2.483 r_scbond_it 1.579 r_mcangle_it 1.378 r_angle_refined_deg 0.963 r_mcbond_it 0.842 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.21 r_metal_ion_refined 0.189 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7481 Nucleic Acid Atoms Solvent Atoms 1166 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing