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High-resolution structure of the extracellular domain of human CD69
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CCK PDB ENTRY 3CCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 301 30% di[polyethyleneglycol]adipate (MW 900), 0.1M Imidazole pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal Properties Matthews coefficient Solvent content 2.19 43.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.067 α = 90 b = 86.067 β = 90 c = 61.975 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 MARMOSAIC 225 mm CCD 2 mirrors and a double-crystal monochromator 2007-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.37 30 94.5 0.054 34.1 7.4 51840 51840 -3 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.37 1.4 65.8 0.588 2.6 5.9 2576
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 ISOMORPHOUS THROUGHOUT PDB ENTRY 3CCK 1.371 28.172 0.09 51820 49718 1982 90.69 0.1351 0.1331 0.1343 0.1836 0.1861 RANDOM 24.7
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] -2.112 -2.112 4.12
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.284 f_angle_d 1.114 f_chiral_restr 0.085 f_bond_d 0.009 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1964 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 6
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling