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Crystal Structure of Reovirus T3D Attachment Protein Sigma1 head domain D345N mutant
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, 20% PEG 8000; protein concentration 8 mg/ml, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.02 α = 90 b = 51.6 β = 95.59 c = 108.86 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 MAR CCD 225 mm undulator 2006-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.85 30 98.7 0.096 9.6 6.5 4.4 79724 78687 -3 15.9
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) 1.85 1.92 97.9 0.416 41.6 1.4 4 7740
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 1.85 30 79724 78676 7920 98.69 0.1801 0.17521 0.1755 0.22364 0.223 RANDOM 17.219
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] -0.39 0.1 0.61 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.304 r_dihedral_angle_4_deg 14.564 r_dihedral_angle_3_deg 12.573 r_dihedral_angle_1_deg 6.359 r_scangle_it 3.686 r_scbond_it 2.496 r_mcangle_it 1.535 r_angle_refined_deg 1.202 r_mcbond_it 0.825 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.304 r_dihedral_angle_4_deg 14.564 r_dihedral_angle_3_deg 12.573 r_dihedral_angle_1_deg 6.359 r_scangle_it 3.686 r_scbond_it 2.496 r_mcangle_it 1.535 r_angle_refined_deg 1.202 r_mcbond_it 0.825 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.272 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.097 r_metal_ion_refined 0.066 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 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 7550 Nucleic Acid Atoms Solvent Atoms 953 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing