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The Closed Headpiece of Integrin IIb 3 and its Complex with an IIb 3 -Specific Antagonist That Does Not Induce Opening
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.9 277 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 259.53 α = 90 b = 144.28 β = 90 c = 104.35 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 300 mm CCD 2008-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.00795 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 50 95.1 0.089 0.089 13.3 5.53 153422 145845
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) 2.4 2.46 95.6 0.956 2.29 5.1 11242
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NID 2.4 48.21 144984 860 95.07 0.17586 0.17563 0.21611 0.2241 RANDOM 13.72
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] -0.45 0.56 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.242 r_dihedral_angle_4_deg 13.598 r_dihedral_angle_3_deg 12.861 r_scangle_it 6.954 r_dihedral_angle_1_deg 5.737 r_scbond_it 4.714 r_mcangle_it 3.155 r_mcbond_it 1.775 r_angle_refined_deg 1.092 r_angle_other_deg 0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.242 r_dihedral_angle_4_deg 13.598 r_dihedral_angle_3_deg 12.861 r_scangle_it 6.954 r_dihedral_angle_1_deg 5.737 r_scbond_it 4.714 r_mcangle_it 3.155 r_mcbond_it 1.775 r_angle_refined_deg 1.092 r_angle_other_deg 0.783 r_mcbond_other 0.363 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20715 Nucleic Acid Atoms Solvent Atoms 790 Heterogen Atoms 361
Software Software Software Name Purpose REFMAC refinement