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Identification of Key residues of the NC6.8 Fab antibody fragment binding to synthetic sweeteners: Crystal structure of NC6.8 co-crystalized with high potency sweetener compound SC45647
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CGS PDB ENTRY 1CGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.2 291 50 mM potassium hydrogen phosphate, 20% polyethylene glycol, pH 9.2, EVAPORATION, temperature 18C, pH 9.20, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.6 α = 90 b = 48.19 β = 109.04 c = 75.35 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 CCD ADSC QUANTUM 4 1999-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 23.64 0.3217 8.8 24844 2.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.9
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 PDB ENTRY 1CGS 2.1 23.64 23597 1246 92.7 0.216 0.213 0.3756 0.277 0.3884 RANDOM 34.62
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] 1.22 3.79 -2.75 4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_4_deg 23.42 r_dihedral_angle_3_deg 18.156 r_dihedral_angle_1_deg 8.681 r_angle_refined_deg 2.459 r_scangle_it 2.408 r_scbond_it 1.677 r_mcangle_it 1.479 r_mcbond_it 0.862 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.054 r_dihedral_angle_4_deg 23.42 r_dihedral_angle_3_deg 18.156 r_dihedral_angle_1_deg 8.681 r_angle_refined_deg 2.459 r_scangle_it 2.408 r_scbond_it 1.677 r_mcangle_it 1.479 r_mcbond_it 0.862 r_nbtor_refined 0.325 r_nbd_refined 0.251 r_symmetry_vdw_refined 0.249 r_symmetry_hbond_refined 0.24 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.155 r_bond_refined_d 0.027 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3345 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 24
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling shake model building REFMAC refinement HKL-2000 data reduction SnB phasing ARP/wARP model building