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Crystal structure of human Signal Regulatory Protein 2 (SIRP) alpha V2 in complex with 5-Hydroxy-L-Tryptophan
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.01M Zinc sulfate heptahydrate
0.1M MES monohydrate pH 6.5
25% v/v PEG monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.457 α = 90 b = 57.457 β = 90 c = 198.156 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 16M 2020-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.5 49.7 100 0.108 1 19.23 25 54272
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 1.167 0.666
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 (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 1.5 49.54 51557 2714 99.98 0.23279 0.23172 0.2387 0.25306 0.264 RANDOM 24.625
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] -0.46 -0.46 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 6.975 r_dihedral_angle_2_deg 6.067 r_long_range_B_refined 5.579 r_long_range_B_other 5.554 r_scangle_other 4.103 r_mcangle_it 3.091 r_mcangle_other 3.091 r_scbond_it 2.687 r_scbond_other 2.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 6.975 r_dihedral_angle_2_deg 6.067 r_long_range_B_refined 5.579 r_long_range_B_other 5.554 r_scangle_other 4.103 r_mcangle_it 3.091 r_mcangle_other 3.091 r_scbond_it 2.687 r_scbond_other 2.685 r_mcbond_it 2.116 r_mcbond_other 2.115 r_angle_refined_deg 1.291 r_angle_other_deg 0.41 r_chiral_restr 0.057 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction