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High-affinity AXL decoy receptor
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 8.4 295 0.7 M Li2SO4, 0.1 M Tris.HCl (pH 8.4)
Crystal Properties Matthews coefficient Solvent content 3.52 65.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.22 α = 90 b = 80.47 β = 90 c = 249.65 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 PIXEL DECTRIS PILATUS 6M Mirrors 2014-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.9795 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.3 38.61 99.6 0.069 0.999 20.14 10.7 69824 -3 59.364
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 97.9 0.886 0.682 1.67 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2C5D 2.3 38.61 66331 3492 99.61 0.2008 0.1984 0.1997 0.2472 0.2427 RANDOM 61.421
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] -2.34 2.58 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.916 r_dihedral_angle_4_deg 20.683 r_dihedral_angle_3_deg 19.442 r_dihedral_angle_1_deg 7.809 r_angle_refined_deg 1.995 r_angle_other_deg 0.926 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.916 r_dihedral_angle_4_deg 20.683 r_dihedral_angle_3_deg 19.442 r_dihedral_angle_1_deg 7.809 r_angle_refined_deg 1.995 r_angle_other_deg 0.926 r_chiral_restr 0.127 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7448 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 61
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing XDS data reduction