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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 = 66.744 α = 90 b = 78.51 β = 106.423 c = 102.021 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 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) 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 1.62 49.62 98.9 0.156 0.169 0.066 0.994 4.86 6.3 62817 15.86
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 1.65 1.68 86.2 2.329 2.657 1.246 0.338 0.2 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6k0y 1.65 49.616 60052 3020 98.926 0.227 0.226 0.2251 0.2568 0.2529 RANDOM 26.485
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] 0.398 0.418 0.592 -1.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.965 r_dihedral_angle_3_deg 14.818 r_dihedral_angle_1_deg 7.843 r_lrange_it 6.859 r_dihedral_angle_2_deg 6.693 r_scangle_it 5.461 r_scbond_it 3.791 r_mcangle_it 3.569 r_mcbond_it 2.468 r_angle_refined_deg 1.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.965 r_dihedral_angle_3_deg 14.818 r_dihedral_angle_1_deg 7.843 r_lrange_it 6.859 r_dihedral_angle_2_deg 6.693 r_scangle_it 5.461 r_scbond_it 3.791 r_mcangle_it 3.569 r_mcbond_it 2.468 r_angle_refined_deg 1.922 r_nbtor_refined 0.31 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.206 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.127 r_gen_planes_refined 0.009 r_bond_refined_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3877 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling PHASER phasing