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Structure of heme transport protein Shr-NEAT2 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, SITTING DROP 8.5 293.15 200 mM Lithium sulfate
100 mM TRIS-HCl
30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.9 57.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.684 α = 90 b = 99.047 β = 90 c = 123.762 γ = 90
Symmetry Space Group I 2 2 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 PILATUS3 S 6M 2023-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 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 2.66 41.47 100 0.063 0.019 1 23.3 12.6 12321
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 2.66 2.79 100 1.01 0.279 0.898 2.6 13.6
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 2.66 41.47 11646 636 99.65 0.21711 0.21466 0.2177 0.26165 0.267 RANDOM 87.122
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] -2.5 -4.51 7.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.302 r_long_range_B_refined 7.522 r_long_range_B_other 7.521 r_dihedral_angle_1_deg 6.938 r_dihedral_angle_2_deg 5.853 r_scangle_other 5.129 r_mcangle_it 4.096 r_mcangle_other 4.095 r_scbond_it 3.673 r_scbond_other 3.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.302 r_long_range_B_refined 7.522 r_long_range_B_other 7.521 r_dihedral_angle_1_deg 6.938 r_dihedral_angle_2_deg 5.853 r_scangle_other 5.129 r_mcangle_it 4.096 r_mcangle_other 4.095 r_scbond_it 3.673 r_scbond_other 3.331 r_mcbond_it 2.741 r_mcbond_other 2.738 r_angle_refined_deg 1.216 r_angle_other_deg 0.424 r_chiral_restr 0.052 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 2438 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing