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Structure of heme transport protein Shr-Linker-NEAT1 from Streptococcus pyogenes in complex with heme.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293.15 200 mM NaCl
100 mM BIS-TRIS
25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.585 α = 90 b = 113.246 β = 96.44 c = 44.281 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS3 S 6M 2025-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 2.35 42.32 99.8 0.137 0.055 0.996 11 7.1 17354
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 99.3 0.697 0.277 0.865 2.8 7.2
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 2.35 42.32 16477 861 99.74 0.21821 0.21579 0.2204 0.26417 0.2684 RANDOM 38.056
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] 32.99 -6.6 -10.3 -22.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.563 r_dihedral_angle_2_deg 7.433 r_long_range_B_other 6.212 r_long_range_B_refined 6.21 r_dihedral_angle_1_deg 6.151 r_scangle_other 4.532 r_mcangle_it 3.679 r_mcangle_other 3.679 r_scbond_it 2.727 r_scbond_other 2.726
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.563 r_dihedral_angle_2_deg 7.433 r_long_range_B_other 6.212 r_long_range_B_refined 6.21 r_dihedral_angle_1_deg 6.151 r_scangle_other 4.532 r_mcangle_it 3.679 r_mcangle_other 3.679 r_scbond_it 2.727 r_scbond_other 2.726 r_mcbond_it 2.364 r_mcbond_other 2.364 r_angle_refined_deg 1.298 r_angle_other_deg 0.435 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 3184 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing