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Structure of complete ectodomain of integrin aIIBb3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JV2 Combination of PDB ENTRY 1JV2 and 1TXV experimental model PDB 1TXV Combination of PDB ENTRY 1JV2 and 1TXV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 10% PEG 3350, 50 mM magnesium acetate, and 0.1 M imidazole, pH 7.0, VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.99 58.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.3 α = 90 b = 81.3 β = 90 c = 654.623 γ = 90
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 ADSC QUANTUM 315 mirrors 2005-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
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 2.55 50 98.6 0.071 0.071 12.17 4.55 135066 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.76 93.9 0.566 0.566 2.13 3.15
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 Combination of PDB ENTRY 1JV2 and 1TXV 2.55 45.31 135027 133242 1785 99.91 0.23332 0.23285 0.2252 0.26802 0.2469 RANDOM 31.839
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_4_deg 9.957 r_dihedral_angle_1_deg 4.263 r_mcangle_it 1.542 r_scangle_it 1.33 r_mcbond_it 0.88 r_scbond_it 0.777 r_angle_refined_deg 0.741 r_angle_other_deg 0.647
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.826 r_dihedral_angle_3_deg 11.482 r_dihedral_angle_4_deg 9.957 r_dihedral_angle_1_deg 4.263 r_mcangle_it 1.542 r_scangle_it 1.33 r_mcbond_it 0.88 r_scbond_it 0.777 r_angle_refined_deg 0.741 r_angle_other_deg 0.647 r_mcbond_other 0.159 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23654 Nucleic Acid Atoms Solvent Atoms 678 Heterogen Atoms 462
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement XDS data reduction XDS data scaling