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Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the Fab fragment of murine monoclonal antibody B5209B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 100 mM sodium citrate tribasic dihydrate (pH 5.6), 10% (w/v) PEG 8000, 10% (v/v) 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.566 α = 90 b = 100.566 β = 90 c = 122.756 γ = 90
Symmetry Space Group P 43 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 ADSC QUANTUM 315 2010-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 50 97.1 56.9 10.4 42067
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 2.07
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 50 39899 2048 97.16 0.23994 0.23801 0.247 0.2782 0.2835 RANDOM 56.661
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] -1.87 -1.87 3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.743 r_dihedral_angle_3_deg 18.583 r_dihedral_angle_4_deg 17.35 r_long_range_B_refined 10.524 r_long_range_B_other 10.522 r_dihedral_angle_1_deg 7.996 r_scangle_other 7.599 r_mcangle_it 7.332 r_mcangle_other 7.331 r_scbond_it 5.586
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.743 r_dihedral_angle_3_deg 18.583 r_dihedral_angle_4_deg 17.35 r_long_range_B_refined 10.524 r_long_range_B_other 10.522 r_dihedral_angle_1_deg 7.996 r_scangle_other 7.599 r_mcangle_it 7.332 r_mcangle_other 7.331 r_scbond_it 5.586 r_scbond_other 5.584 r_mcbond_it 5.469 r_mcbond_other 5.468 r_angle_refined_deg 2.102 r_angle_other_deg 1.118 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 3931 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building PHASER phasing