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Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the scFv fragment of murine monoclonal antibody B5209B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 85mM Tris-HCl (pH 8.5), 27.5% (w/v) PEG 4000, 170mM lithium sulfate monohydrate, 670mM sodium thiocyanate, 15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.42 49.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.69 α = 90 b = 149.943 β = 90 c = 66.153 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX225HE 2011-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 95.1 11.9 3.8 39986
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 2.1 2.18
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 MOLECULAR REPLACEMENT THROUGHOUT 2.1 50 37871 1979 95.16 0.24104 0.2388 0.2438 0.28476 0.2837 RANDOM 26.513
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] -0.58 -0.87 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_3_deg 17.887 r_dihedral_angle_4_deg 17.111 r_dihedral_angle_1_deg 8.93 r_long_range_B_refined 6.911 r_long_range_B_other 6.868 r_scangle_other 4.235 r_mcangle_it 3.306 r_mcangle_other 3.306 r_scbond_other 2.691
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_3_deg 17.887 r_dihedral_angle_4_deg 17.111 r_dihedral_angle_1_deg 8.93 r_long_range_B_refined 6.911 r_long_range_B_other 6.868 r_scangle_other 4.235 r_mcangle_it 3.306 r_mcangle_other 3.306 r_scbond_other 2.691 r_scbond_it 2.69 r_mcbond_it 2.095 r_mcbond_other 2.089 r_angle_refined_deg 1.834 r_angle_other_deg 1.057 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4869 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building PHASER phasing