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Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 Tri-HCl, 20% Ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.62 53.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.873 α = 90 b = 66.415 β = 90 c = 105.692 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate MIRROR 2007-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 55.9 99.9 0.035 13.3 20 52135
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.7
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 2PI6 1.65 27.711 50989 1075 99.88 0.1385 0.13756 0.1514 0.1876 0.1961 RANDOM 23.707
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] 0.13 -0.41 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.048 r_dihedral_angle_4_deg 21.857 r_dihedral_angle_3_deg 12.785 r_long_range_B_other 7.301 r_long_range_B_refined 7.299 r_dihedral_angle_1_deg 6.637 r_scangle_other 3.633 r_angle_refined_deg 2.892 r_scbond_it 2.432 r_scbond_other 2.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.048 r_dihedral_angle_4_deg 21.857 r_dihedral_angle_3_deg 12.785 r_long_range_B_other 7.301 r_long_range_B_refined 7.299 r_dihedral_angle_1_deg 6.637 r_scangle_other 3.633 r_angle_refined_deg 2.892 r_scbond_it 2.432 r_scbond_other 2.431 r_mcangle_other 2.401 r_mcangle_it 2.399 r_angle_other_deg 1.763 r_mcbond_it 1.556 r_mcbond_other 1.541 r_chiral_restr 0.204 r_bond_refined_d 0.035 r_gen_planes_refined 0.018 r_bond_other_d 0.005 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2876 Nucleic Acid Atoms Solvent Atoms 599 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing