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crystal structure of ICAM-5 in complex with aL I domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T0P PDB IDS 1T0P AND 1IC1 experimental model PDB 1IC1 PDB IDS 1T0P AND 1IC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 296 0.1M HEPES pH7.5, 7.5%PEG8000, 10%glycerol, 5mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties Matthews coefficient Solvent content 3.73 66.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.793 α = 90 b = 71.507 β = 90 c = 143.871 γ = 90
Symmetry Space Group P 21 21 21
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97931 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 2.099 71.98 98.6 0.072 0.054 8.2 37303 33.3
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 2.099 2.18 95.5 0.454 0.471 3.76 5.6 3564
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 (All) 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 THROUGHOUT PDB IDS 1T0P AND 1IC1 2.099 71.98 37303 37303 1863 98.03 0.193 0.193 0.191 0.2005 0.235 0.2386 RANDOM 43.703
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] -0.71 4.05 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.189 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_3_deg 13.285 r_dihedral_angle_1_deg 5.929 r_scangle_it 4.104 r_mcangle_it 3.484 r_mcbond_it 2.855 r_scbond_it 2.709 r_angle_refined_deg 1.32 r_angle_other_deg 0.816
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.189 r_dihedral_angle_4_deg 13.636 r_dihedral_angle_3_deg 13.285 r_dihedral_angle_1_deg 5.929 r_scangle_it 4.104 r_mcangle_it 3.484 r_mcbond_it 2.855 r_scbond_it 2.709 r_angle_refined_deg 1.32 r_angle_other_deg 0.816 r_mcbond_other 0.531 r_symmetry_vdw_other 0.22 r_symmetry_hbond_refined 0.218 r_nbd_refined 0.201 r_nbd_other 0.189 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.156 r_symmetry_vdw_refined 0.105 r_nbtor_other 0.1 r_chiral_restr 0.075 r_metal_ion_refined 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3000 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing