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Crystal structure of apo HpsK from Bilophila wadsworthia
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, Tris, pH 8.5, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.17 43.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.017 α = 90 b = 87.806 β = 108.841 c = 65.954 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 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 2.01 48.41 98.2 0.99 6.6 7.1 39014
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 2.01 2.06 0.64
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 2.006 35.936 38993 1989 97.995 0.177 0.1747 0.1828 0.2275 0.2318 RANDOM 21.294
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] 0.244 -0.757 1.379 -0.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.524 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_2_deg 7.357 r_dihedral_angle_1_deg 6.045 r_lrange_it 4.743 r_lrange_other 4.708 r_scangle_it 3.848 r_scangle_other 3.847 r_scbond_it 2.368 r_scbond_other 2.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.524 r_dihedral_angle_3_deg 14.002 r_dihedral_angle_2_deg 7.357 r_dihedral_angle_1_deg 6.045 r_lrange_it 4.743 r_lrange_other 4.708 r_scangle_it 3.848 r_scangle_other 3.847 r_scbond_it 2.368 r_scbond_other 2.368 r_mcangle_it 2.127 r_mcangle_other 2.127 r_angle_refined_deg 1.437 r_mcbond_it 1.424 r_mcbond_other 1.424 r_angle_other_deg 0.5 r_nbd_refined 0.217 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.183 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.169 r_symmetry_xyhbond_nbd_refined 0.145 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 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 4867 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing