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Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F11 pdb entries 1F11, 1P53 experimental model PDB 1P53 pdb entries 1F11, 1P53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.5M LITHIUM SULFATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.49 64.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.396 α = 90 b = 69.342 β = 112.76 c = 88.173 γ = 90
Symmetry Space Group C 1 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 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97949 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 2.7 30 90.6 0.087 0.087 11.1 3.5 26015 26015
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 2.7 2.8 58.1 0.543 0.543 1.2 2.7
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 entries 1F11, 1P53 2.7 28.5 25959 23400 2559 100 0.209 0.204 0.204 0.253 0.2502 RANDOM 63.34
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] -5.52 -4.12 6.95 -4.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.831 r_dihedral_angle_4_deg 12.788 r_dihedral_angle_3_deg 10.599 r_dihedral_angle_1_deg 4.96 r_angle_refined_deg 0.903 r_mcangle_it 0.897 r_scangle_it 0.865 r_angle_other_deg 0.656 r_mcbond_it 0.627 r_scbond_it 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.831 r_dihedral_angle_4_deg 12.788 r_dihedral_angle_3_deg 10.599 r_dihedral_angle_1_deg 4.96 r_angle_refined_deg 0.903 r_mcangle_it 0.897 r_scangle_it 0.865 r_angle_other_deg 0.656 r_mcbond_it 0.627 r_scbond_it 0.49 r_nbd_other 0.164 r_nbtor_refined 0.163 r_symmetry_vdw_other 0.153 r_nbd_refined 0.149 r_symmetry_vdw_refined 0.093 r_chiral_restr 0.091 r_xyhbond_nbd_refined 0.091 r_metal_ion_refined 0.09 r_symmetry_hbond_refined 0.088 r_nbtor_other 0.077 r_symmetry_metal_ion_refined 0.066 r_mcbond_other 0.016 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other 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 5234 Nucleic Acid Atoms Solvent Atoms 276 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing