8QZB | pdb_00008qzb

D-2-hydroxyacid dehydrogenase (D2HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid, NAD+ and chloride (1.16 A resolution)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5MH6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8290Protein 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 coefficientSolvent content
2.5551.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.182α = 109.074
b = 74.777β = 107.882
c = 78.172γ = 95.56
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2023-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9801DiamondI03

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
11.1646.63393.90.0420.9417.13.6427918
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)
11.161.1883.70.50.563.3

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)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.1646.6334278832134293.8970.1360.13460.1330.16510.163614.538
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]
0.041-0.179-0.0920.2430.081-0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it20.022
r_lrange_other18.124
r_dihedral_angle_6_deg17.509
r_scangle_it14.943
r_scangle_other14.942
r_dihedral_angle_3_deg12.192
r_scbond_it11.645
r_scbond_other11.644
r_mcangle_it11.423
r_mcangle_other11.422
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_it20.022
r_lrange_other18.124
r_dihedral_angle_6_deg17.509
r_scangle_it14.943
r_scangle_other14.942
r_dihedral_angle_3_deg12.192
r_scbond_it11.645
r_scbond_other11.644
r_mcangle_it11.423
r_mcangle_other11.422
r_dihedral_angle_2_deg11.294
r_mcbond_it9.115
r_mcbond_other9.111
r_dihedral_angle_1_deg6.448
r_rigid_bond_restr4.983
r_angle_refined_deg1.689
r_angle_other_deg0.706
r_symmetry_nbd_refined0.277
r_symmetry_xyhbond_nbd_refined0.236
r_nbd_refined0.228
r_nbd_other0.203
r_metal_ion_refined0.198
r_nbtor_refined0.174
r_symmetry_nbd_other0.172
r_xyhbond_nbd_refined0.133
r_chiral_restr0.096
r_symmetry_nbtor_other0.073
r_dihedral_angle_other_2_deg0.065
r_symmetry_xyhbond_nbd_other0.052
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_xyhbond_nbd_other0.005
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 Atoms1619
Heterogen Atoms266

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing