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D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid, NAD+ and chloride (1.16 A resolution)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 Protein buffer:
20mM Tris/HCl pH 8.0
2mM EDTA
1M NaCl
50mM 2-ketohexanoic acid
5mM NAD+
Crystallisation conditions:
0.1M Tris/HCl pH 8.0
0.5M Magnesium acetate
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.182 α = 109.074 b = 74.777 β = 107.882 c = 78.172 γ = 95.56
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 XE 16M 2023-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9801 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 1.16 46.633 93.9 0.042 0.94 17.1 3.6 427918
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 1.16 1.18 83.7 0.5 0.56 3.3
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.16 46.633 427883 21342 93.897 0.136 0.1346 0.133 0.1651 0.1636 14.538
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] 0.041 -0.179 -0.092 0.243 0.081 -0.159
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.022 r_lrange_other 18.124 r_dihedral_angle_6_deg 17.509 r_scangle_it 14.943 r_scangle_other 14.942 r_dihedral_angle_3_deg 12.192 r_scbond_it 11.645 r_scbond_other 11.644 r_mcangle_it 11.423 r_mcangle_other 11.422
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 20.022 r_lrange_other 18.124 r_dihedral_angle_6_deg 17.509 r_scangle_it 14.943 r_scangle_other 14.942 r_dihedral_angle_3_deg 12.192 r_scbond_it 11.645 r_scbond_other 11.644 r_mcangle_it 11.423 r_mcangle_other 11.422 r_dihedral_angle_2_deg 11.294 r_mcbond_it 9.115 r_mcbond_other 9.111 r_dihedral_angle_1_deg 6.448 r_rigid_bond_restr 4.983 r_angle_refined_deg 1.689 r_angle_other_deg 0.706 r_symmetry_nbd_refined 0.277 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.228 r_nbd_other 0.203 r_metal_ion_refined 0.198 r_nbtor_refined 0.174 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.073 r_dihedral_angle_other_2_deg 0.065 r_symmetry_xyhbond_nbd_other 0.052 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_xyhbond_nbd_other 0.005 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 1619 Heterogen Atoms 266
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing