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Structure of human CD47 in complex with human signal regulatory protein (SIRP) alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJS PDB ENTRY 2JJS CHAINS A AND C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 278 100 NL SIRP ALPHA / CD47 COMPLEX (1:1 RATIO, EACH PROTEIN AT APPROX. 0.375 UM) PLUS 100 NL RESERVOIR (0.1 M CITRATE PH 5.0, 30% W/V PEG 3000) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 5 C.
Crystal Properties Matthews coefficient Solvent content 2.07 33.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.62 α = 90 b = 63.72 β = 90 c = 123.02 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 CCD MARRESEARCH MIRRORS 2006-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 40 99.5 0.19 7.4 7 19339 -3 31.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.45 98.5 0.57 3.9 6.7
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 PDB ENTRY 2JJS CHAINS A AND C 2.3 26.81 18293 989 99.5 0.238 0.235 0.2411 0.288 0.2887 RANDOM 24.7
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] -2.62 4.4 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.081 r_dihedral_angle_4_deg 14.203 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 6.564 r_scangle_it 1.266 r_angle_refined_deg 1.193 r_scbond_it 0.842 r_angle_other_deg 0.821 r_mcangle_it 0.465 r_mcbond_it 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.081 r_dihedral_angle_4_deg 14.203 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 6.564 r_scangle_it 1.266 r_angle_refined_deg 1.193 r_scbond_it 0.842 r_angle_other_deg 0.821 r_mcangle_it 0.465 r_mcbond_it 0.322 r_symmetry_vdw_other 0.276 r_nbd_other 0.194 r_nbtor_refined 0.17 r_nbd_refined 0.168 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.133 r_symmetry_hbond_refined 0.126 r_nbtor_other 0.091 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3506 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing