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CD40 in complex with Bleselumab Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FAX experimental model PDB 3Z3K experimental model PDB 4M6O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 0.2 M Ammonium chloride
20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.565 α = 90 b = 116.002 β = 91.713 c = 121.651 γ = 90
Symmetry Space Group P 1 21 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 PILATUS3 S 6M 2021-12-20 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 2.7 45.56 99.9 0.143 0.059 0.996 12.8 6.8 37822
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 2.7 2.8 100 0.941 0.537 0.824 2.3 6.9
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 2.7 45.56 37802 1858 99.865 0.207 0.204 0.2088 0.2651 0.2677 52.149
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] -1.872 -1.951 2.942 -0.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.614 r_dihedral_angle_6_deg 13.886 r_dihedral_angle_2_deg 10.349 r_dihedral_angle_1_deg 8.502 r_lrange_other 5.089 r_lrange_it 5.088 r_scangle_it 3.538 r_scangle_other 3.538 r_mcangle_it 3.262 r_mcangle_other 3.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.614 r_dihedral_angle_6_deg 13.886 r_dihedral_angle_2_deg 10.349 r_dihedral_angle_1_deg 8.502 r_lrange_other 5.089 r_lrange_it 5.088 r_scangle_it 3.538 r_scangle_other 3.538 r_mcangle_it 3.262 r_mcangle_other 3.262 r_scbond_it 2.158 r_scbond_other 2.158 r_mcbond_it 2.014 r_mcbond_other 2.013 r_angle_refined_deg 1.56 r_angle_other_deg 0.537 r_nbd_other 0.231 r_symmetry_nbd_other 0.216 r_xyhbond_nbd_refined 0.212 r_nbd_refined 0.202 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.181 r_symmetry_xyhbond_nbd_refined 0.093 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.006 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 8812 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing