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Crystal structure of the LT1009 (SONEPCIZUMAB) antibody Fab fragment in complex with sphingosine-1-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291.15 1 microliter of 12 mg/mL S1P:Fab complex was mixed with 1 microliter and sealed over 1 mL of reservoir solution containing 22% (w/v) polyethylene glycol 3350, 100 mM MgSO4, 100 mM sodium citrate (pH 6.0) and 10% (v/v) ethylene glycol., VAPOR DIFFUSION, HANGING DROP, temperature 291.15K
Crystal Properties Matthews coefficient Solvent content 3.42 64.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.052 α = 90 b = 70.889 β = 90 c = 138.719 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 ADSC QUANTUM 210 2008-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97741 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.9 50 97 0.055 26.4 5.1 52056 50494 3.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 76.8 0.409 2.18 3.3 3940
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 1.9 50 50430 2548 96.96 0.192 0.19 0.1813 0.219 0.2032 RANDOM 28.232
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] 0.54 -1.26 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.921 r_dihedral_angle_4_deg 21.612 r_dihedral_angle_3_deg 15.264 r_dihedral_angle_1_deg 8.849 r_scangle_it 3.37 r_scbond_it 2.102 r_angle_refined_deg 1.542 r_mcangle_it 1.506 r_mcbond_it 0.913 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.921 r_dihedral_angle_4_deg 21.612 r_dihedral_angle_3_deg 15.264 r_dihedral_angle_1_deg 8.849 r_scangle_it 3.37 r_scbond_it 2.102 r_angle_refined_deg 1.542 r_mcangle_it 1.506 r_mcbond_it 0.913 r_nbtor_refined 0.299 r_metal_ion_refined 0.223 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.11 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3361 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 32
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling