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CRYSTAL STRUCTURE OF vhh-based FAB-fragment of antibody BCD-085
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I1K 5I1K, 5FGB experimental model PDB 5FGB 5I1K, 5FGB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 50 mM Na-Ac pH 5.5, 150 mM NaCl with 1.5 M (NH4)2SO4, 150 mM sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.56 α = 90 b = 111.92 β = 90 c = 165.43 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 PIXEL DECTRIS PILATUS3 S 6M 2018-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 99.9 0.053 19.2 6.2 132510
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 1.9 1.95
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 5I1K, 5FGB 1.9 47.6 125855 6624 99.7 0.17173 0.16872 0.174 0.22802 0.2294 RANDOM 48.813
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] 0.45 -0.65 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.042 r_sphericity_free 32.781 r_sphericity_bonded 21.487 r_dihedral_angle_4_deg 20.309 r_dihedral_angle_3_deg 14.823 r_long_range_B_refined 9.198 r_long_range_B_other 9.169 r_scangle_other 8.055 r_mcangle_it 7.787 r_mcangle_other 7.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.042 r_sphericity_free 32.781 r_sphericity_bonded 21.487 r_dihedral_angle_4_deg 20.309 r_dihedral_angle_3_deg 14.823 r_long_range_B_refined 9.198 r_long_range_B_other 9.169 r_scangle_other 8.055 r_mcangle_it 7.787 r_mcangle_other 7.787 r_scbond_it 6.794 r_rigid_bond_restr 6.738 r_scbond_other 6.607 r_mcbond_it 6.428 r_mcbond_other 6.426 r_dihedral_angle_1_deg 6.418 r_angle_refined_deg 1.291 r_angle_other_deg 1.186 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 13122 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing