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Crystal structure of HpsK from Ruegeria pomeroyi 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 6.5
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.793 α = 90 b = 68.756 β = 120.323 c = 71.377 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 2025-10-05 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 1.65 42.208 99.9 1 16.1 5.2 42559
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 1.65 1.68 1
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 1.65 42.208 42559 2150 99.887 0.142 0.1406 0.1532 0.1639 0.1722 RANDOM 12.41
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] 0.284 -0.417 0.722 -0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.416 r_dihedral_angle_3_deg 10.824 r_dihedral_angle_1_deg 6.367 r_dihedral_angle_2_deg 6.184 r_lrange_it 4.341 r_lrange_other 3.999 r_scangle_it 2.703 r_scangle_other 2.702 r_scbond_it 1.725 r_scbond_other 1.724
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.416 r_dihedral_angle_3_deg 10.824 r_dihedral_angle_1_deg 6.367 r_dihedral_angle_2_deg 6.184 r_lrange_it 4.341 r_lrange_other 3.999 r_scangle_it 2.703 r_scangle_other 2.702 r_scbond_it 1.725 r_scbond_other 1.724 r_angle_refined_deg 1.498 r_mcangle_other 1.322 r_mcangle_it 1.319 r_mcbond_it 0.882 r_mcbond_other 0.88 r_angle_other_deg 0.534 r_nbd_refined 0.212 r_nbtor_refined 0.184 r_symmetry_nbd_other 0.183 r_symmetry_xyhbond_nbd_refined 0.159 r_xyhbond_nbd_refined 0.155 r_symmetry_nbd_refined 0.119 r_nbd_other 0.115 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.074 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 423 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing