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Crystal structure of the 139H2 Fab fragment bound to Muc1 peptide epitope
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold By ColabFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 0.2M NaCl
20%w/v PEG 8K
0.1M Na Phos Cit pH 4.2
Crystal Properties Matthews coefficient Solvent content 2.56 51.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.833 α = 90 b = 42.757 β = 122.306 c = 129.064 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 PIXEL DECTRIS EIGER2 X CdTe 9M 2023-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.6199 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.5 56.117 100 0.387 0.399 0.093 0.988 9 18.2 34554
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 2.5 2.6 100 1.813 1.876 0.478 0.689 0.7 15.3
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 56.117 34554 1758 99.945 0.206 0.2031 0.2538 0.2035 32.858
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] 0.556 0.246 -0.684 -0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.966 r_dihedral_angle_3_deg 16.104 r_dihedral_angle_2_deg 8.414 r_dihedral_angle_1_deg 8.008 r_lrange_it 4.202 r_lrange_other 4.181 r_scangle_it 2.884 r_scangle_other 2.884 r_mcangle_it 2.459 r_mcangle_other 2.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.966 r_dihedral_angle_3_deg 16.104 r_dihedral_angle_2_deg 8.414 r_dihedral_angle_1_deg 8.008 r_lrange_it 4.202 r_lrange_other 4.181 r_scangle_it 2.884 r_scangle_other 2.884 r_mcangle_it 2.459 r_mcangle_other 2.459 r_scbond_it 1.709 r_scbond_other 1.708 r_mcbond_it 1.429 r_mcbond_other 1.429 r_angle_refined_deg 1.325 r_angle_other_deg 0.441 r_symmetry_xyhbond_nbd_refined 0.242 r_symmetry_nbd_other 0.201 r_nbd_refined 0.195 r_nbd_other 0.191 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.162 r_ncsr_local_group_1 0.097 r_symmetry_nbtor_other 0.089 r_ncsr_local_group_2 0.08 r_symmetry_xyhbond_nbd_other 0.073 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6719 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction Aimless data scaling PHASER phasing