☰ Navigation Tabs
CD28 in complex with the antibody Fab fragment AI3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UTA experimental model PDB 6O8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 Crystallization trials were set up using the CD28-AI3 Fab at 15.8 mg/mL in phosphate buffered saline (PBS) pH 7.4. Drops were set up using 100 nl protein and 100 nL reservoir solution containing 200 mM zinc acetate, 0.1 M imidazole pH 8.0, 20% w/v PEG 3000.
Crystal Properties Matthews coefficient Solvent content 2.63 53.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.874 α = 90 b = 117.939 β = 90 c = 145.719 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.999873 MAX IV BioMAX
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 3.05 91.843 100 0.243 0.268 0.112 0.995 8.2 10.3 25981
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 3.05 3.26 1.912 2.112 0.884 0.602 10.5
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 3.05 91.843 25926 1327 99.969 0.201 0.1975 0.1974 0.2575 0.255 91.441
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] 7.175 -5.263 -1.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.976 r_lrange_other 15.785 r_lrange_it 15.784 r_dihedral_angle_6_deg 14.974 r_scangle_it 12.172 r_scangle_other 12.171 r_mcangle_it 10.17 r_mcangle_other 10.169 r_scbond_it 8.117 r_scbond_other 8.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.976 r_lrange_other 15.785 r_lrange_it 15.784 r_dihedral_angle_6_deg 14.974 r_scangle_it 12.172 r_scangle_other 12.171 r_mcangle_it 10.17 r_mcangle_other 10.169 r_scbond_it 8.117 r_scbond_other 8.116 r_mcbond_it 6.864 r_mcbond_other 6.863 r_dihedral_angle_1_deg 5.844 r_dihedral_angle_2_deg 4.267 r_angle_refined_deg 1.687 r_angle_other_deg 0.586 r_nbd_other 0.256 r_symmetry_xyhbond_nbd_refined 0.248 r_symmetry_nbd_refined 0.218 r_symmetry_nbd_other 0.2 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.177 r_metal_ion_refined 0.137 r_ncsr_local_group_3 0.113 r_symmetry_metal_ion_refined 0.109 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.078 r_symmetry_xyhbond_nbd_other 0.071 r_ncsr_local_group_1 0.057 r_ncsr_local_group_2 0.051 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8507 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 251
Software Software Software Name Purpose REFMAC refinement REFMAC refinement EDNA data collection XDS data reduction Aimless data scaling PHASER phasing