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Structure of the immunoglobulin-superfamily ectodomain of human CD47
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJS PDB ENTRY 2JJS, CHAIN C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 200 NL 17 MG/ML CD47 PLUS 100 NL RESERVOIR (0.2 M MGCL2, 0.1 M BIS-TRIS PH 5.5, 25% W/V PEG 3350) EQUILIBRATED AGAINST 95 UL OF RESERVOIR AT 20.5 C.
Crystal Properties Matthews coefficient Solvent content 2.6 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.137 α = 90 b = 47.502 β = 99.31 c = 56.811 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 CCD MARRESEARCH MIRRORS 2006-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.9 28.3 98.8 0.07 13.9 3.7 41496 -3 24.9
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 1.9 2 91.8 0.4 2.9 3.1
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 (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, CHAIN C 1.9 28.19 39392 2100 98.6 0.219 0.216 0.219 0.263 0.2645 RANDOM 25.59
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] 0.07 0.15 -0.76 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_4_deg 14.853 r_dihedral_angle_3_deg 13.381 r_dihedral_angle_1_deg 6.621 r_scangle_it 2.133 r_scbond_it 1.411 r_angle_refined_deg 1.367 r_angle_other_deg 0.847 r_mcangle_it 0.769 r_mcbond_it 0.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.938 r_dihedral_angle_4_deg 14.853 r_dihedral_angle_3_deg 13.381 r_dihedral_angle_1_deg 6.621 r_scangle_it 2.133 r_scbond_it 1.411 r_angle_refined_deg 1.367 r_angle_other_deg 0.847 r_mcangle_it 0.769 r_mcbond_it 0.621 r_symmetry_vdw_other 0.2 r_nbd_other 0.196 r_nbd_refined 0.181 r_nbtor_refined 0.176 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.15 r_symmetry_vdw_refined 0.136 r_nbtor_other 0.108 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_bond_other_d 0.004 r_gen_planes_refined 0.004 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 3647 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing