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Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model SwissModel
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 Magnesium chloride hexahydrate
calcium chloride dihydrate
NDSB
sodium HEPES
MOPS
ethylene glycol
PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.41 63.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.779 α = 90 b = 74.779 β = 90 c = 392.355 γ = 120
Symmetry Space Group P 65 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 2023-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.85 20 99.9 0.027 0.999 12 16.1 57161
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 100 0.827 0.473 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.85 19.77 54692 2305 99.86 0.23101 0.22952 0.2373 0.26739 0.274 RANDOM 53.69
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] 0.62 0.31 0.62 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.464 r_dihedral_angle_3_deg 15.763 r_long_range_B_refined 9.147 r_long_range_B_other 9.126 r_dihedral_angle_1_deg 7.491 r_scangle_other 7.317 r_mcangle_it 5.252 r_mcangle_other 5.251 r_scbond_it 5.15 r_scbond_other 5.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.464 r_dihedral_angle_3_deg 15.763 r_long_range_B_refined 9.147 r_long_range_B_other 9.126 r_dihedral_angle_1_deg 7.491 r_scangle_other 7.317 r_mcangle_it 5.252 r_mcangle_other 5.251 r_scbond_it 5.15 r_scbond_other 5.149 r_mcbond_it 3.979 r_mcbond_other 3.978 r_angle_refined_deg 1.76 r_angle_other_deg 0.616 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3258 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing