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Crystal structure of apo HpsK from Ruegeria pomeroyi, Crystal form 2
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, Bis-Tris, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.849 α = 90 b = 126.101 β = 117.289 c = 58.834 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 2025-04-13 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 1.9 48.792 99.6 1 11.5 3.5 55825
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 1.9 1.94 0.94
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 1.897 48.792 55792 2874 99.524 0.161 0.1594 0.1702 0.1985 0.2083 RANDOM 16.749
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] 0.993 -0.234 0.984 -1.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.516 r_dihedral_angle_3_deg 11.398 r_dihedral_angle_1_deg 6.393 r_dihedral_angle_2_deg 4.958 r_lrange_it 4.304 r_lrange_other 4.137 r_scangle_other 3.12 r_scangle_it 3.117 r_scbond_it 1.981 r_scbond_other 1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.516 r_dihedral_angle_3_deg 11.398 r_dihedral_angle_1_deg 6.393 r_dihedral_angle_2_deg 4.958 r_lrange_it 4.304 r_lrange_other 4.137 r_scangle_other 3.12 r_scangle_it 3.117 r_scbond_it 1.981 r_scbond_other 1.981 r_mcangle_it 1.74 r_mcangle_other 1.74 r_angle_refined_deg 1.461 r_mcbond_it 1.207 r_mcbond_other 1.207 r_angle_other_deg 0.519 r_nbd_refined 0.215 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.182 r_nbd_other 0.15 r_xyhbond_nbd_refined 0.145 r_symmetry_nbd_refined 0.086 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.075 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 5106 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing