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Crystal structure of human BAFF in complex with Fab fragment of anti-BAFF antibody belimumab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KD7 1KD7 , 7FAB experimental model PDB 7FAB 1KD7 , 7FAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 9% (w/v) PEG4000, 0.1 M MgCl2, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.26 62.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.687 α = 90 b = 135.499 β = 91.88 c = 138.18 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2016-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1 SLS X06SA
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 2.9 138.11 98.7 11.24 3.36 109365
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 2.9 3.15 95.4 3.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1KD7 , 7FAB 2.9 138.11 108711 654 99.01 0.19106 0.19082 0.1946 0.23128 0.2351 RANDOM 59.251
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] 0.89 -1.56 0.29 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.688 r_dihedral_angle_4_deg 16.333 r_dihedral_angle_3_deg 13.846 r_dihedral_angle_1_deg 7.616 r_long_range_B_refined 6.105 r_long_range_B_other 6.104 r_scangle_other 4.689 r_mcangle_it 3.571 r_mcangle_other 3.571 r_scbond_it 3.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.688 r_dihedral_angle_4_deg 16.333 r_dihedral_angle_3_deg 13.846 r_dihedral_angle_1_deg 7.616 r_long_range_B_refined 6.105 r_long_range_B_other 6.104 r_scangle_other 4.689 r_mcangle_it 3.571 r_mcangle_other 3.571 r_scbond_it 3.125 r_scbond_other 3.125 r_mcbond_it 2.222 r_mcbond_other 2.222 r_angle_refined_deg 1.524 r_angle_other_deg 1.197 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 25879 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing