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The crystal structure of simian CD163 SRCR5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Bis-Tris pH5.5, 25% PEG 3350, 0.2M NaCl
Crystal Properties Matthews coefficient Solvent content 1.81 31.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.623 α = 71.02 b = 33.465 β = 75.29 c = 46.726 γ = 84.91
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS3 6M 2017-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 1.58 50 95.1 0.04 24.6 3.4 20604
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 1.58 1.64 0.096
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 1BY2 1.58 31.66 19537 1063 94.8 0.16 0.158 0.1676 0.193 0.2001 RANDOM 13.92
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] 0.08 -0.03 -0.01 -0.02 0.06 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.164 r_dihedral_angle_4_deg 17.974 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_1_deg 7.451 r_long_range_B_refined 5.235 r_long_range_B_other 4.969 r_scangle_other 2.456 r_mcangle_it 1.85 r_mcangle_other 1.85 r_scbond_it 1.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.164 r_dihedral_angle_4_deg 17.974 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_1_deg 7.451 r_long_range_B_refined 5.235 r_long_range_B_other 4.969 r_scangle_other 2.456 r_mcangle_it 1.85 r_mcangle_other 1.85 r_scbond_it 1.584 r_scbond_other 1.583 r_angle_refined_deg 1.169 r_mcbond_it 1.094 r_mcbond_other 1.092 r_angle_other_deg 0.937 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1578 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction HKL-3000 data scaling HKL-3000 phasing