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The Thrombospondin-1 Polymorphism Asn700Ser Associated with Cornoary Artery Disease Causes Local and Long-Ranging Changes in Protein Structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YO8 PDB ENTRY 1YO8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 25% PEG [4000], 0.2M sodium acetate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.23 61.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.892 α = 90 b = 122.65 β = 90 c = 155.381 γ = 90
Symmetry Space Group I 2 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 100 CCD BRUKER SMART 2000 2006-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.9 80 0.137 9.7 6.8 19186 19888
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 2.9 3 0.372 3 6.8 18897
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 (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 PDB ENTRY 1YO8 2.9 30 19172 18868 1019 98.02 0.22943 0.22687 0.2268 0.27671 0.2784 RANDOM 38.017
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] -3.41 -1.59 4.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.959 r_dihedral_angle_3_deg 16.361 r_dihedral_angle_4_deg 14.541 r_dihedral_angle_1_deg 6.127 r_mcangle_it 1.098 r_angle_refined_deg 1.052 r_scangle_it 0.76 r_mcbond_it 0.627 r_scbond_it 0.498 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.959 r_dihedral_angle_3_deg 16.361 r_dihedral_angle_4_deg 14.541 r_dihedral_angle_1_deg 6.127 r_mcangle_it 1.098 r_angle_refined_deg 1.052 r_scangle_it 0.76 r_mcbond_it 0.627 r_scbond_it 0.498 r_nbtor_refined 0.33 r_symmetry_vdw_refined 0.283 r_nbd_refined 0.26 r_symmetry_hbond_refined 0.23 r_xyhbond_nbd_refined 0.203 r_metal_ion_refined 0.186 r_chiral_restr 0.078 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_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 4850 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 86
Software Software Software Name Purpose AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling