☰ Navigation Tabs
CD40 in complex with Dacetuzumab Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P3I experimental model PDB 7RT9 experimental model PDB 3HR5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Ammonium citrate tribasic pH 7.0
20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 3.78 67.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.194 α = 90 b = 208.172 β = 90 c = 198.061 γ = 90
Symmetry Space Group C 2 2 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 PILATUS3 S 6M 2022-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 49.8 100 0.151 0.042 0.999 17.3 13.7 101033
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 100 1.35 0.375 0.813 2.1 13.8
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 THROUGHOUT 2.8 49.8 100999 4995 99.974 0.212 0.209 0.2132 0.2617 0.2615 67.037
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] 3.065 -4.423 1.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.748 r_dihedral_angle_6_deg 13.796 r_lrange_it 9.786 r_lrange_other 9.785 r_dihedral_angle_1_deg 7.866 r_mcangle_it 7.383 r_mcangle_other 7.383 r_scangle_it 7.048 r_scangle_other 7.048 r_dihedral_angle_2_deg 6.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.748 r_dihedral_angle_6_deg 13.796 r_lrange_it 9.786 r_lrange_other 9.785 r_dihedral_angle_1_deg 7.866 r_mcangle_it 7.383 r_mcangle_other 7.383 r_scangle_it 7.048 r_scangle_other 7.048 r_dihedral_angle_2_deg 6.196 r_mcbond_it 4.769 r_mcbond_other 4.767 r_scbond_it 4.494 r_scbond_other 4.493 r_angle_refined_deg 1.377 r_angle_other_deg 0.475 r_xyhbond_nbd_refined 0.249 r_nbd_refined 0.204 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.179 r_nbd_other 0.158 r_symmetry_nbd_refined 0.121 r_symmetry_xyhbond_nbd_other 0.112 r_symmetry_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.061 r_chiral_restr_other 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16768 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing