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Crystal structure of the anti-PAS Fab 2.2 in complex with its epitope peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 11% (w/v) PEG 6000
100 mM Tris/HCl pH 8
200 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.996 α = 90 b = 121.996 β = 90 c = 138.437 γ = 90
Symmetry Space Group I 4 2 2
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 Si mirror 2019-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
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 2.55 34.63 99.9 0.209 0.213 0.998 16.98 26.176 17370 28.843
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 2.55 2.65 100 0.736 0.751 0.949 5.12 25.171
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 3QQ9 2.55 34.63 16545 825 99.9 0.1971 0.1951 0.2019 0.2376 0.2394 RANDOM 27.208
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] -2.27 -2.27 4.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.896 r_dihedral_angle_4_deg 19.771 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 8.129 r_angle_refined_deg 1.327 r_angle_other_deg 1.135 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.896 r_dihedral_angle_4_deg 19.771 r_dihedral_angle_3_deg 14.479 r_dihedral_angle_1_deg 8.129 r_angle_refined_deg 1.327 r_angle_other_deg 1.135 r_chiral_restr 0.045 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3418 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction