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PD1 signaling receptor bound to FAB Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K0Y experimental model PDB 6CNR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 20.5% PEG 3350, 0.4M
MgCl2, 0.1M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.161 α = 104.8 b = 53.794 β = 101.825 c = 103.003 γ = 92.57
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 16M 2022-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.03 51.85 98.03 0.1322 0.9918 11.11 3.63 67042
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.03 2.06 95.11 1.2855 0.222 1.07 3.71
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 2.03 51.848 67042 3094 97.977 0.213 0.21 0.2139 0.2755 0.2788 34.071
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] 0.938 0.164 -0.974 1.624 -1.175 -1.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.906 r_dihedral_angle_6_deg 13.737 r_dihedral_angle_1_deg 8.48 r_dihedral_angle_2_deg 8.299 r_lrange_it 6.993 r_lrange_other 6.985 r_scangle_it 5.256 r_scangle_other 5.255 r_mcangle_it 4.491 r_mcangle_other 4.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.906 r_dihedral_angle_6_deg 13.737 r_dihedral_angle_1_deg 8.48 r_dihedral_angle_2_deg 8.299 r_lrange_it 6.993 r_lrange_other 6.985 r_scangle_it 5.256 r_scangle_other 5.255 r_mcangle_it 4.491 r_mcangle_other 4.491 r_scbond_it 3.512 r_scbond_other 3.511 r_mcbond_it 3.081 r_mcbond_other 3.081 r_angle_refined_deg 1.785 r_angle_other_deg 0.614 r_symmetry_nbd_other 0.206 r_nbd_refined 0.204 r_nbd_other 0.192 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.172 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.13 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.088 r_symmetry_xyhbond_nbd_other 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8163 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing