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Structure of Fab-Fragment GB11 agains tumour associated carbohydrate antigens.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XTG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 DL-Malic acid, Citric acid, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.16 α = 90 b = 109.16 β = 90 c = 40.268 γ = 90
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 PILATUS 6M 2021-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.86 54.58 100 0.202 0.211 0.086 7.7 11.6 40412
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.9 100 2.721 2.852 0.847 0.376 0.9 11.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.86 48.866 40382 1959 99.928 0.202 0.2004 0.1988 0.2387 0.2382 35.946
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] 0.988 0.988 -1.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.46 r_dihedral_angle_3_deg 16.098 r_dihedral_angle_2_deg 9.84 r_dihedral_angle_1_deg 8.397 r_lrange_it 7.48 r_lrange_other 7.48 r_scangle_it 5.001 r_scangle_other 5.001 r_scbond_it 3.611 r_scbond_other 3.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.46 r_dihedral_angle_3_deg 16.098 r_dihedral_angle_2_deg 9.84 r_dihedral_angle_1_deg 8.397 r_lrange_it 7.48 r_lrange_other 7.48 r_scangle_it 5.001 r_scangle_other 5.001 r_scbond_it 3.611 r_scbond_other 3.61 r_mcangle_other 3.302 r_mcangle_it 3.301 r_mcbond_it 2.213 r_mcbond_other 2.21 r_angle_refined_deg 1.804 r_angle_other_deg 0.643 r_nbd_refined 0.194 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.132 r_nbd_other 0.127 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.083 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3306 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 138
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing