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Crystal structure of HpsK from Ruegeria pomeroyi in complex with R-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 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.791 α = 90 b = 69.464 β = 120.42 c = 71.473 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2025-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 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 1.96 48.07 99.7 1 12.1 3.5 25729
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 1.96 2.01 0.93
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 1.958 42.218 25729 1218 99.605 0.146 0.1439 0.1577 0.1779 0.1825 RANDOM 14.476
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] -0.234 -0.527 0.892 -0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.409 r_dihedral_angle_3_deg 11.526 r_dihedral_angle_1_deg 6.402 r_dihedral_angle_2_deg 5.08 r_lrange_it 4.745 r_lrange_other 4.52 r_scangle_it 3.168 r_scangle_other 3.167 r_scbond_other 1.982 r_scbond_it 1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.409 r_dihedral_angle_3_deg 11.526 r_dihedral_angle_1_deg 6.402 r_dihedral_angle_2_deg 5.08 r_lrange_it 4.745 r_lrange_other 4.52 r_scangle_it 3.168 r_scangle_other 3.167 r_scbond_other 1.982 r_scbond_it 1.981 r_mcangle_other 1.515 r_mcangle_it 1.513 r_angle_refined_deg 1.427 r_mcbond_it 0.999 r_mcbond_other 0.998 r_angle_other_deg 0.504 r_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.197 r_nbtor_refined 0.183 r_symmetry_nbd_other 0.181 r_xyhbond_nbd_refined 0.147 r_nbd_other 0.097 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.072 r_symmetry_nbd_refined 0.032 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2461 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing