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Structure of a chimeric antibody (Fab) fragment bound to de-N-acetyl polysialic acid (dPSA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel The search model was obtained by homology modeling (Swiss-Model) using the coordinates from PDB entry 6pe7 and the sequence of the Fab that was in this crystal.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 24% polyethylene glycol 1,500; 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.57 52.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.585 α = 90 b = 71.437 β = 92.954 c = 91.495 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 PILATUS3 S 6M 2021-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.0 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.83 74.49 99.9 0.081 0.999 9.1 6.8 84628 33.59
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 99.9 0.364 0.8 6.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6pe7 1.83 74.49 84628 1458 99.84 0.1856 0.1854 0.2297 0.2308 39.29
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] 2.90316975 -2.27503165 -1.75152163 -1.15164812
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.3184 s_dihedral_angle_3_deg 10.6468 s_dihedral_angle_1_deg 7.3934 s_dihedral_angle_2_deg 6.4542 s_angle_nonh_deg 2.0623 s_nbtor 0.2259 s_nbd 0.2136 s_symmetry_nbd 0.1907 s_symmetry_hbond_nbd 0.1733 s_hbond_nbd 0.1482
RMS Deviations Key Refinement Restraint Deviation s_dihedral_angle_6_deg 15.3184 s_dihedral_angle_3_deg 10.6468 s_dihedral_angle_1_deg 7.3934 s_dihedral_angle_2_deg 6.4542 s_angle_nonh_deg 2.0623 s_nbtor 0.2259 s_nbd 0.2136 s_symmetry_nbd 0.1907 s_symmetry_hbond_nbd 0.1733 s_hbond_nbd 0.1482 s_chiral_restr 0.0893 s_bond_nonh_d 0.0124 s_planes 0.0103
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6567 Nucleic Acid Atoms Solvent Atoms 407 Heterogen Atoms 263
Software Software Software Name Purpose Servalcat refinement XDS data reduction SCALEPACK data scaling PHASER phasing