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Crystal structure of a first-in-class antibody for alpha-1,6-fucosylated prostate-specific antigen, target bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZTP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 100 mM Tris-HCl pH 8.5, 6.25% v/v PEG 3350, 6.25% v/v PEG 4000, 6.25% v/v PEG 2000 and 6.25% v/v PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.31 α = 90 b = 87.395 β = 90 c = 150.427 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 80 PIXEL DECTRIS EIGER2 X 16M 2021-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.38 52.24 95.7 0.054 0.999 15.7 6.7 155757 27.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.49 65.4 1.169 0.633 1.5 7.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.38 41.2 1.35 155639 7799 79.42 0.1564 0.1547 0.1571 0.1865 0.1886 23.82
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.3607 f_angle_d 0.7665 f_chiral_restr 0.0757 f_bond_d 0.0051 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6672 Nucleic Acid Atoms Solvent Atoms 795 Heterogen Atoms 24
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing