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Crystal structure of the complex of signalling protein from sheep (SPS-40) with a designed peptide Trp-His-Trp reveals significance of Asn79 and Trp191 in the complex formation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2V pdb entry 1r2v
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 25mM tris HCl,50mM NaCl, 11% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.79 α = 90 b = 66.309 β = 90 c = 107.382 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 298 IMAGE PLATE MARRESEARCH MIRROR 2004-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 3.5 56 89.1 0.2 4.5 5105 35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.56 85.1 0.59 2.1
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1r2v 3.5 56 5105 4869 236 84.8 0.18 0.17764 0.17601 0.21035 RANDOM 25.56
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] -1.85 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.238 r_scangle_it 4.662 r_scbond_it 2.649 r_mcangle_it 2.019 r_angle_refined_deg 2.005 r_dihedral_angle_1_deg 1.917 r_angle_other_deg 1.374 r_mcbond_it 1.049 r_nbtor_other 0.54 r_symmetry_vdw_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.238 r_scangle_it 4.662 r_scbond_it 2.649 r_mcangle_it 2.019 r_angle_refined_deg 2.005 r_dihedral_angle_1_deg 1.917 r_angle_other_deg 1.374 r_mcbond_it 1.049 r_nbtor_other 0.54 r_symmetry_vdw_refined 0.298 r_nbd_refined 0.288 r_symmetry_vdw_other 0.284 r_symmetry_hbond_refined 0.256 r_nbd_other 0.255 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.137 r_xyhbond_nbd_other 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 r_bond_other_d 0.004 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_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 2907 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing