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Recognition of peptide ligands by signalling protein from porcine mammary gland (SPP-40): Crystal structure of the complex of SPP-40 with a peptide Trp-Pro-Trp at 2.45A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XRV PDB ENTRY 1xrv
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 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.38 α = 90 b = 66.79 β = 90 c = 107.66 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 2004-10-14 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 2.45 20 95.2 0.077 9.7 17202 16643 26.5
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 2.45 2.49 96.1 0.412 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 PDB ENTRY 1xrv 2.45 20 17202 16304 339 95.2 0.194 0.193 0.192 0.226 RANDOM 33.8
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] -2.58 -2.44 5.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 24.6 x_scangle_it 4.711 x_mcangle_it 3.298 x_scbond_it 3.187 x_mcbond_it 1.998 r_angle_refined_deg 1.6 x_dihedral_angle_d 1.11 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2947 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling AMoRE phasing CNS refinement HKL-2000 data reduction