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Crystal structure of the complete integrin alhaVbeta3 ectodomain plus an Alpha/beta transmembrane fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JV2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 298 12% PEG3350, 0.1M Na acetate, 0.8M NaCl, 2.5mM CaCl2, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 4.05 69.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.87 α = 90 b = 129.87 β = 90 c = 305.9 γ = 120
Symmetry Space Group P 32 2 1
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 2009-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-ID
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 2.9 50 93 0.088 8.9 5 66702 1 1
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 1JV2 2.9 20 59083 59083 2917 100 0.24637 0.24447 0.2441 0.28482 0.2958 RANDOM 45.773
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] -1.45 -0.73 -1.45 2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.54 r_dihedral_angle_3_deg 17.241 r_dihedral_angle_4_deg 11.941 r_dihedral_angle_1_deg 6.415 r_scangle_it 1.476 r_angle_refined_deg 1.13 r_angle_other_deg 0.808 r_scbond_it 0.74 r_mcangle_it 0.455 r_mcbond_it 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.54 r_dihedral_angle_3_deg 17.241 r_dihedral_angle_4_deg 11.941 r_dihedral_angle_1_deg 6.415 r_scangle_it 1.476 r_angle_refined_deg 1.13 r_angle_other_deg 0.808 r_scbond_it 0.74 r_mcangle_it 0.455 r_mcbond_it 0.243 r_nbd_refined 0.198 r_nbd_other 0.176 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.148 r_symmetry_vdw_other 0.147 r_metal_ion_refined 0.13 r_symmetry_vdw_refined 0.123 r_symmetry_hbond_refined 0.099 r_nbtor_other 0.092 r_chiral_restr 0.065 r_mcbond_other 0.028 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_xyhbond_nbd_other 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other 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 12632 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 455
Software Software Software Name Purpose REFMAC refinement CNS refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing