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Structure of porcine torovirus Hemagglutinin-Esterase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CL4 PDB ENTRY 3CL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2M potassium acetate, 18% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 3.15 60.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.307 α = 90 b = 104.528 β = 95.79 c = 97.473 γ = 90
Symmetry Space Group C 1 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 ADSC QUANTUM 4 2007-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.1 58 100 0.116 8.4 3.8 90957 90957 -3.7 28.7
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 2.1 2.21 100 0.721 2.2 3.8 13238
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 3CL4 2.1 48.49 90955 86400 4555 100 0.17252 0.17081 0.1814 0.20463 0.2112 RANDOM 16.673
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] -1.15 0.3 0.48 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.532 r_dihedral_angle_4_deg 14.379 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_1_deg 7.07 r_scangle_it 3.547 r_scbond_it 2.207 r_angle_refined_deg 1.567 r_mcangle_it 1.187 r_angle_other_deg 0.918 r_mcbond_it 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.532 r_dihedral_angle_4_deg 14.379 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_1_deg 7.07 r_scangle_it 3.547 r_scbond_it 2.207 r_angle_refined_deg 1.567 r_mcangle_it 1.187 r_angle_other_deg 0.918 r_mcbond_it 0.66 r_mcbond_other 0.175 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8487 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 236
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling