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Crystal structure of human Fab A194-01 in complex with its synthetic tetrasaccharide Ara4 epitope (BSI110886)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Human Fab structures
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 285 Optimization screen around RigakuReagents JCSG+ B12, condition D5: 200mM potassium citrate, 18.6% (w/V) PEG 3350: HosaA.20194.b.K13.PC00170 at 19.5mg/ml + 1mMYB-8-099 / BSI110866 cryo: 20% EG + 1mM compound: tray: 312856d5: puck: zmt3-1
Crystal Properties Matthews coefficient Solvent content 3.02 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.62 α = 90 b = 149.01 β = 99.506 c = 114.53 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 2019-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.45 50 99 0.088 0.105 0.995 10.49 3.223 102834 41.192
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 2.45 2.51 98.8 0.593 0.709 0.775 2.03 3.247
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 human Fab structures 2.45 45.47 1.36 102796 1982 98.97 0.1687 0.1677 0.1711 0.2176 0.2197 0 48.03
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 18.2613 f_angle_d 0.8405 f_chiral_restr 0.0522 f_plane_restr 0.0047 f_bond_d 0.0042
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16090 Nucleic Acid Atoms Solvent Atoms 1131 Heterogen Atoms 250
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing Coot model building