9IBE | pdb_00009ibe

D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with potassium, 2-ketohexanoic acid, NADP+ and chloride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8QZBsearch with dimer of domain 2 (find 2 copies) and single domain 1 (find 4 copies)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8290protein 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 coefficientSolvent content
2.5952.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.633α = 108.841
b = 75.34β = 108.084
c = 78.234γ = 95.526
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.940535DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.2652.392.20.0590.99123.833281911.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.261.2889.40.990.330.83.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2652.2763328071670092.2340.1540.15180.15980.18760.1924Random18.037
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]
0.33-0.178-0.2160.1910.214-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.692
r_lrange_other16.816
r_dihedral_angle_6_deg16.326
r_scangle_it15.12
r_scangle_other15.119
r_dihedral_angle_2_deg13.176
r_scbond_it11.646
r_scbond_other11.646
r_dihedral_angle_3_deg10.379
r_mcangle_other10.013
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it17.692
r_lrange_other16.816
r_dihedral_angle_6_deg16.326
r_scangle_it15.12
r_scangle_other15.119
r_dihedral_angle_2_deg13.176
r_scbond_it11.646
r_scbond_other11.646
r_dihedral_angle_3_deg10.379
r_mcangle_other10.013
r_mcangle_it10.012
r_mcbond_it7.814
r_mcbond_other7.811
r_dihedral_angle_1_deg6.681
r_rigid_bond_restr4.08
r_dihedral_angle_other_2_deg3.434
r_angle_refined_deg1.837
r_angle_other_deg0.784
r_symmetry_nbd_refined0.268
r_nbd_refined0.248
r_nbd_other0.186
r_symmetry_xyhbond_nbd_refined0.186
r_symmetry_nbd_other0.168
r_nbtor_refined0.168
r_metal_ion_refined0.131
r_xyhbond_nbd_refined0.129
r_chiral_restr0.099
r_symmetry_nbtor_other0.072
r_symmetry_xyhbond_nbd_other0.05
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9396
Nucleic Acid Atoms
Solvent Atoms1569
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing