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Crystal structure of apo HpsK from Ruegeria pomeroyi, crystal form 1
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, HANGING DROP 293 PEG3350, sodium formate
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.02 α = 72.289 b = 58.87 β = 70.895 c = 67.7 γ = 62.75
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 2025-04-13 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 1.47 46.83 96.2 1 18.5 3.9 112178
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 1.47 1.5 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 1.472 46.826 112178 5558 96.147 0.132 0.1305 0.1372 0.1598 0.1619 RANDOM 18.395
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] -1.266 3.48 -6.725 0.422 1.997 0.845
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.454 r_lrange_it 13.287 r_lrange_other 11.483 r_dihedral_angle_3_deg 11.193 r_dihedral_angle_2_deg 8.721 r_scangle_it 7.85 r_scangle_other 7.849 r_dihedral_angle_1_deg 6.094 r_mcangle_it 5.859 r_mcangle_other 5.859
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.454 r_lrange_it 13.287 r_lrange_other 11.483 r_dihedral_angle_3_deg 11.193 r_dihedral_angle_2_deg 8.721 r_scangle_it 7.85 r_scangle_other 7.849 r_dihedral_angle_1_deg 6.094 r_mcangle_it 5.859 r_mcangle_other 5.859 r_scbond_it 5.439 r_scbond_other 5.438 r_mcbond_it 4.084 r_mcbond_other 4.082 r_rigid_bond_restr 2.618 r_angle_refined_deg 1.494 r_symmetry_xyhbond_nbd_other 0.661 r_angle_other_deg 0.556 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.181 r_symmetry_nbd_refined 0.174 r_nbd_other 0.162 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.076 r_gen_planes_refined 0.008 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 5114 Nucleic Acid Atoms Solvent Atoms 815 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing