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Crystal structure of HpsK from Bilophila wadsworthia in complex with S-DHPS (2,3-dihydroxypropanesulfonate)
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 293 PEG3350, Bis-Tris, pH 5.5, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.27 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.753 α = 70.309 b = 52.048 β = 88.754 c = 66.644 γ = 80.142
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 2025-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.827 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.05 46.659 94.7 1 11.3 3.6 285217
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.05 1.07 0.86
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 (All) 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 1.05 46.659 285216 14616 94.724 0.119 0.1178 0.1178 0.1361 0.1361 RANDOM 11.197
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] 0.181 0.139 -0.104 0.067 -0.088 -0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.17 r_dihedral_angle_3_deg 12.121 r_lrange_it 12.108 r_lrange_other 9.853 r_scangle_it 7.435 r_scangle_other 7.435 r_dihedral_angle_2_deg 7.406 r_dihedral_angle_1_deg 6.054 r_scbond_other 5.329 r_scbond_it 5.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.17 r_dihedral_angle_3_deg 12.121 r_lrange_it 12.108 r_lrange_other 9.853 r_scangle_it 7.435 r_scangle_other 7.435 r_dihedral_angle_2_deg 7.406 r_dihedral_angle_1_deg 6.054 r_scbond_other 5.329 r_scbond_it 5.328 r_mcangle_other 4.439 r_mcangle_it 4.43 r_rigid_bond_restr 4.196 r_mcbond_it 3.221 r_mcbond_other 3.205 r_angle_refined_deg 1.907 r_angle_other_deg 0.674 r_symmetry_nbd_refined 0.3 r_symmetry_xyhbond_nbd_other 0.268 r_nbd_other 0.261 r_nbd_refined 0.253 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.184 r_symmetry_xyhbond_nbd_refined 0.152 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4981 Nucleic Acid Atoms Solvent Atoms 857 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing