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Crystal structure of the scavenger receptor cysteine-rich domain 5 (SRCR5) from porcine CD163
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 4.6 298 25% (w/v) PEG 4000, 200mM (NH4)2SO4, 100mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.96 37.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.72 α = 90 b = 73.01 β = 90 c = 87.4 γ = 90
Symmetry Space Group C 2 2 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 6M 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 29.1 97.7 29.1 13.1 8953
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1BY2 1.8 29.1 8487 443 97.24 0.21495 0.213 0.25341 0.2727 RANDOM 16.37
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] -0.57 -0.95 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.722 r_dihedral_angle_4_deg 17.037 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 7.579 r_long_range_B_refined 5.114 r_long_range_B_other 4.349 r_mcangle_it 1.876 r_mcangle_other 1.876 r_scangle_other 1.814 r_angle_refined_deg 1.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.722 r_dihedral_angle_4_deg 17.037 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 7.579 r_long_range_B_refined 5.114 r_long_range_B_other 4.349 r_mcangle_it 1.876 r_mcangle_other 1.876 r_scangle_other 1.814 r_angle_refined_deg 1.333 r_scbond_it 1.105 r_scbond_other 1.104 r_mcbond_it 1.08 r_mcbond_other 1.075 r_angle_other_deg 0.925 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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 737 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection XDS data scaling