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Crystal structure of human CD47 in complex with engineered SIRPa.D1(N80A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TZ2 5TZ2, 2JJS experimental model PDB 2JJS 5TZ2, 2JJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 30% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.14 60.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.58 α = 90 b = 99.64 β = 90 c = 138.93 γ = 90
Symmetry Space Group P 21 21 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 X 6M 2022-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935 APS 19-ID
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 2.76 47.19 100 0.288 0.309 0.109 0.977 10.1 8.5 19839
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 2.76 2.91 99.9 1.419 1.523 0.542 0.517 8.2
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 (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 5TZ2, 2JJS 2.76 47.19 18821 964 99.92 0.2196 0.2173 0.2177 0.2648 0.2683 RANDOM 49.453
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] -1.97 -1.69 3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.904 r_dihedral_angle_4_deg 19.075 r_dihedral_angle_3_deg 14.634 r_dihedral_angle_1_deg 7.189 r_angle_refined_deg 1.214 r_angle_other_deg 1.074 r_chiral_restr 0.034 r_bond_refined_d 0.003 r_bond_other_d 0.003 r_gen_planes_refined 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.904 r_dihedral_angle_4_deg 19.075 r_dihedral_angle_3_deg 14.634 r_dihedral_angle_1_deg 7.189 r_angle_refined_deg 1.214 r_angle_other_deg 1.074 r_chiral_restr 0.034 r_bond_refined_d 0.003 r_bond_other_d 0.003 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3611 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing