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Crystal structure of the ternary complex of signalling glycoprotein frm sheep (SPS-40)with hexasaccharide (NAG6) and peptide Trp-Pro-Trp at 3.0A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R2V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 25mM tris-HCl, 11% ethanol , pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.72 54.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.497 α = 90 b = 66.624 β = 90 c = 107.481 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 2005-08-22 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 20 99.8 0.11 6.8 9481 58.8
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 3.12 98.7 0.282 2.2
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 1r2v 3 19.88 9481 9269 212 98.6 0.2066 0.206 0.206 0.23 RANDOM 38.6
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] -6.29 -3.86 10.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 5.8 c_scbond_it 3.96 c_mcangle_it 3.51 c_mcbond_it 2.09 c_angle_deg 1.7 c_improper_angle_d 1.01 c_bond_d 0.01 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 5.8 c_scbond_it 3.96 c_mcangle_it 3.51 c_mcbond_it 2.09 c_angle_deg 1.7 c_improper_angle_d 1.01 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2905 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 113
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing