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Structure of headpiece of integrin aIIBb3 in open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VDR PDB ENTRY 2VDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 10% PEG 8000, 0.4 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.66 73.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 332.093 α = 90 b = 332.093 β = 90 c = 88.288 γ = 120
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 210 MIRROR 2003-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
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 2.9 50 98.3 0.097 0.097 17.4 10 122126
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 2.9 3 93.9 0.602 0.602 3 6
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 2VDR 2.9 44.59 118478 115380 3098 95.21 0.17436 0.17373 0.1766 0.19741 0.197 RANDOM 60.195
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.407 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_4_deg 11.57 r_dihedral_angle_1_deg 5.541 r_scangle_it 4.194 r_mcangle_it 3.887 r_scbond_it 2.536 r_mcbond_it 2.238 r_angle_refined_deg 0.657 r_angle_other_deg 0.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.407 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_4_deg 11.57 r_dihedral_angle_1_deg 5.541 r_scangle_it 4.194 r_mcangle_it 3.887 r_scbond_it 2.536 r_mcbond_it 2.238 r_angle_refined_deg 0.657 r_angle_other_deg 0.645 r_mcbond_other 0.361 r_chiral_restr 0.049 r_bond_refined_d 0.006 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 20990 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 323
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling