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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 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 260.67 α = 90 b = 145.17 β = 90 c = 104.44 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 2009-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97948 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 2.25 50 99.9 0.094 0.094 12.11 6.63 187880 187671
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) 2.25 2.31 99.9 0.994 1.9 5.98 13781
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3NID 2.25 48.491 1.99 187662 1009 99.9 0.1719 0.1717 0.1621 0.212 0.2018
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] -2.0843 3.0583 -0.974
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.385 f_angle_d 1.153 f_chiral_restr 0.071 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20735 Nucleic Acid Atoms Solvent Atoms 1227 Heterogen Atoms 224
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling