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D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with potassium, 2-ketohexanoic acid, NADP+ and chloride
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8QZB search with dimer of domain 2 (find 2 copies) and single domain 1 (find 4 copies)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 protein buffer:
20 mM Tris/HCl pH 8.0
2 mM EDTA
1 M KCl
50 mM 2-ketohexanoic acid
5 mM NAD+
Well Solution:
0.1 M Mg acetate
26 % PEG 3350
0.1 M Tris/HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.633 α = 108.841 b = 75.34 β = 108.084 c = 78.234 γ = 95.526
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 EIGER2 X 16M 2023-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.940535 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.26 52.3 92.2 0.059 0.99 12 3.8 332819 11.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 89.4 0.99 0.33 0.8 3.8
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 1.26 52.276 332807 16700 92.234 0.154 0.1518 0.1598 0.1876 0.1924 Random 18.037
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] 0.33 -0.178 -0.216 0.191 0.214 -0.32
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.692 r_lrange_other 16.816 r_dihedral_angle_6_deg 16.326 r_scangle_it 15.12 r_scangle_other 15.119 r_dihedral_angle_2_deg 13.176 r_scbond_it 11.646 r_scbond_other 11.646 r_dihedral_angle_3_deg 10.379 r_mcangle_other 10.013
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 17.692 r_lrange_other 16.816 r_dihedral_angle_6_deg 16.326 r_scangle_it 15.12 r_scangle_other 15.119 r_dihedral_angle_2_deg 13.176 r_scbond_it 11.646 r_scbond_other 11.646 r_dihedral_angle_3_deg 10.379 r_mcangle_other 10.013 r_mcangle_it 10.012 r_mcbond_it 7.814 r_mcbond_other 7.811 r_dihedral_angle_1_deg 6.681 r_rigid_bond_restr 4.08 r_dihedral_angle_other_2_deg 3.434 r_angle_refined_deg 1.837 r_angle_other_deg 0.784 r_symmetry_nbd_refined 0.268 r_nbd_refined 0.248 r_nbd_other 0.186 r_symmetry_xyhbond_nbd_refined 0.186 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.168 r_metal_ion_refined 0.131 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.05 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9396 Nucleic Acid Atoms Solvent Atoms 1569 Heterogen Atoms 268
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing