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Crystal structure of the anti-PAS Fab 1.2 in complex with its epitope peptide and the anti-Kappa VHH domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O2Z 7O2Z, 6ANA experimental model PDB 6ANA 7O2Z, 6ANA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% (w/v) PEG 3350
300 mM K-acetate
Crystal Properties Matthews coefficient Solvent content 2.17 43.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.296 α = 90 b = 44.373 β = 109.14 c = 93.032 γ = 90
Symmetry Space Group C 1 2 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 2M 2019-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91840 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 33.39 97.2 0.058 0.063 0.999 15.03 6.923 77314 30.697
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.65 95.8 0.988 1.07 0.792 1.64 6.777
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 7O2Z, 6ANA 1.55 33.39 73508 3884 97.32 0.1962 0.1943 0.2046 0.2323 0.2387 RANDOM 26.694
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] -1.53 -0.99 0.44 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.361 r_dihedral_angle_4_deg 19.944 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 7.57 r_angle_refined_deg 1.685 r_angle_other_deg 1.403 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.361 r_dihedral_angle_4_deg 19.944 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 7.57 r_angle_refined_deg 1.685 r_angle_other_deg 1.403 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4343 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction