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Crystal structure of the Fab fragment of B5209B, a murine monoclonal antibody specific for the fifth immunoglobulin domain (Ig5) of human ROBO1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM sodium cacodylate trihydrate (pH 6.5), 29% (w/v) PEG 8000, 200 mM ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.48 50.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.431 α = 90 b = 83.947 β = 90 c = 129.498 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 CCD RAYONIX MX225HE 2011-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 SPring-8 BL32XU
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 1.5 50 99 24.9 6.5 73816
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 1.5 1.55
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 1.5 50 70018 3752 98.67 0.13095 0.12917 0.1311 0.1651 0.1669 RANDOM 28.692
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] -1.6 1.23 0.37
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.271 r_dihedral_angle_2_deg 36.744 r_sphericity_bonded 21.352 r_dihedral_angle_4_deg 18.228 r_dihedral_angle_3_deg 14.274 r_long_range_B_refined 8.457 r_long_range_B_other 8.457 r_dihedral_angle_1_deg 7.217 r_scangle_other 6.695 r_scbond_other 6.134
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 41.271 r_dihedral_angle_2_deg 36.744 r_sphericity_bonded 21.352 r_dihedral_angle_4_deg 18.228 r_dihedral_angle_3_deg 14.274 r_long_range_B_refined 8.457 r_long_range_B_other 8.457 r_dihedral_angle_1_deg 7.217 r_scangle_other 6.695 r_scbond_other 6.134 r_scbond_it 6.128 r_rigid_bond_restr 6.094 r_mcangle_other 5.263 r_mcangle_it 5.262 r_mcbond_it 4.855 r_mcbond_other 4.848 r_angle_refined_deg 2.599 r_angle_other_deg 1.956 r_chiral_restr 0.338 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_gen_planes_other 0.008 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3228 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building PHASER phasing