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Crystal structure of the ApoER2 ectodomain in complex with the Reelin R56 fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 11-12.5%(wt./vol.) PEG 3350 200-250mM sodium thiocyanate, 20mM HEPES-Na (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 3.59 65.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.951 α = 90 b = 205.951 β = 90 c = 169.84 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 ADSC QUANTUM 315r 2008-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97904 Photon Factory BL-5A
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 3.2 49.52 100 0.139 0.997 16.4 14.8 67441
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.28
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 3.2 49.52 63926 3467 99.97 0.20277 0.19999 0.1985 0.25481 0.2545 RANDOM 99.77
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] 2.07 2.07 2.07 -6.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.446 r_dihedral_angle_3_deg 16.674 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_1_deg 6.942 r_angle_refined_deg 1.178 r_chiral_restr 0.082 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.446 r_dihedral_angle_3_deg 16.674 r_dihedral_angle_4_deg 15.215 r_dihedral_angle_1_deg 6.942 r_angle_refined_deg 1.178 r_chiral_restr 0.082 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18806 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling autoSHARP phasing