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An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C5D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.4 M Li2SO4, 0.1 M Tris.HCl(pH 8.5), 5% Glycerol, 2mM NiSO4 , VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 5.02 75.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.37 α = 90 b = 112.37 β = 90 c = 361.26 γ = 120
Symmetry Space Group P 32 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 315r Rh coated flat mirror. 2012-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.03317 SSRL BL7-1
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 3.07 38.01 99.9 0.118 20.4 11.9 50640 50592
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 3.07 3.15 100 1 2.11 7.1 3664
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C5D 3.07 38.01 47994 47994 2526 99.92 0.20416 0.20214 0.24255 0.2189 RANDOM 91.547
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] -0.41 -0.41 -0.41 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_3_deg 18.008 r_dihedral_angle_4_deg 16.084 r_dihedral_angle_1_deg 6.78 r_angle_refined_deg 1.282 r_angle_other_deg 0.728 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.599 r_dihedral_angle_3_deg 18.008 r_dihedral_angle_4_deg 16.084 r_dihedral_angle_1_deg 6.78 r_angle_refined_deg 1.282 r_angle_other_deg 0.728 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8845 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms 71
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling