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Crystal structure of human Fab A194-01 in complex with its synthetic heptasaccharide Ara6-Man epitope (BSI110888)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T1W D_1000261517
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 285 Optimization screen around RigakuReagents JCSG+ B12, condition A8: 200mM potassium citrate tribasic, 21.4% (w/V) PEG 3350: HosaA.20194.b.K13.PC00170 at 19.5mg/ml + 1mM YB-8-150 / BSI110868 cryo: 20% EG + 1mM compound: tray: 312860 A8: puck: nmo4-9
Crystal Properties Matthews coefficient Solvent content 3.06 59.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.93 α = 90 b = 149.26 β = 99.315 c = 115.36 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 CCD RAYONIX MX-300 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.6 50 99.4 0.106 0.124 0.993 10.46 3.713 87616 39.427
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 2.6 2.67 95.2 0.573 0.707 0.693 1.75 2.758
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE D_1000261517 2.6 28.03 1.35 87524 2039 99.41 0.1607 0.1594 0.1631 0.2157 0.2155 0 48.55
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 17.9131 f_angle_d 0.9958 f_chiral_restr 0.059 f_bond_d 0.006 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16099 Nucleic Acid Atoms Solvent Atoms 873 Heterogen Atoms 354
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction PHENIX phasing Coot model building