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2.7 A structure of the extracellular domains of the human beta common receptor involved in IL-3, IL-5, and GM-CSF signalling
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GH7 pdb entry 1gh7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 277 10% polyethylene glycol 5000 mono-methyl ether in phosphate buffer, pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.47 64.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.909 α = 90 b = 184.909 β = 90 c = 101.047 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 MAR CCD 165 mm 2004-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.117 APS 14-ID-B
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 2.7 50 91.4 0.06 19.2 5.96 35381 32327 45.3
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 2.7 2.8 40.2 0.153 2.4
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 FOURIER SYNTHESIS THROUGHOUT pdb entry 1gh7 2.7 50 35381 30934 1392 91.36 0.21426 0.21426 0.21169 0.2089 0.26913 0.2665 RANDOM 51.114
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] -1.16 -0.58 -1.16 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.832 r_dihedral_angle_3_deg 22.321 r_dihedral_angle_4_deg 21.065 r_dihedral_angle_1_deg 8.299 r_scangle_it 3.557 r_angle_refined_deg 2.217 r_scbond_it 2.171 r_mcangle_it 1.35 r_mcbond_it 0.75 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.832 r_dihedral_angle_3_deg 22.321 r_dihedral_angle_4_deg 21.065 r_dihedral_angle_1_deg 8.299 r_scangle_it 3.557 r_angle_refined_deg 2.217 r_scbond_it 2.171 r_mcangle_it 1.35 r_mcbond_it 0.75 r_nbtor_refined 0.33 r_symmetry_hbond_refined 0.31 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.218 r_chiral_restr 0.167 r_xyhbond_nbd_refined 0.164 r_bond_refined_d 0.022 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6280 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing