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Crystal structure of native octameric SAP-like pentraxin from Limulus polyphemus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QTJ Rigid body refinement of polyalanine model of native octameric Limulus SAP, PDB code 1qtj
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 298 Tris, NaCl, pH 7.4, sitting drop, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.9 68.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.33 α = 90 b = 173.33 β = 90 c = 98.81 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 FILM CEA 1989-01-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX7.2 1.488 SRS PX7.2
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 3 60.9 89 0.117 4 13666 13666
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) 3 3.13 55.6 0.284
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 (All) 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 THROUGHOUT Rigid body refinement of polyalanine model of native octameric Limulus SAP, PDB code 1qtj 3 60.9 13564 674 88.2 0.214 0.214 0.184 0.1849 0.232 0.1928 Random 30.711
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] -1.147 -1.147 2.295
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.831 c_mcangle_it 2.156 c_scbond_it 1.768 c_mcbond_it 1.214
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3336 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction MOSFLM data reduction ROTAVATA/AGROVATA data scaling