☰ Navigation Tabs
Crystal structure of human 4-1BB/TNFRSF9 in complex with the anti-4-1BB DARPin protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.10 M Citric acid pH=5.00
1.60 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.13 60.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.33 α = 90 b = 102.469 β = 91.54 c = 167.366 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 EIGER X 16M 2020-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999953 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.81 167.31 92.4 0.157 0.157 7.1 4.3 47018
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.815 3.173 60.1 1.042 1.042 1.5 4.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.81 167.31 44690 2328 67.15 0.2436 0.2412 0.2425 0.2912 0.2881 RANDOM 55.416
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] 0.22 -0.16 -0.23 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.615 r_dihedral_angle_4_deg 19.699 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_1_deg 9.028 r_mcangle_it 5.643 r_mcbond_it 3.374 r_mcbond_other 3.373 r_angle_refined_deg 1.55 r_angle_other_deg 1.224 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.615 r_dihedral_angle_4_deg 19.699 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_1_deg 9.028 r_mcangle_it 5.643 r_mcbond_it 3.374 r_mcbond_other 3.373 r_angle_refined_deg 1.55 r_angle_other_deg 1.224 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15363 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 283
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing