5MH5

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 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: 20 mM Tris-HCl pH8, 3 mM EDTA and 1 M NaCl Crystallisation condition: 0.1 M Tris-HCl pH8, 0.5 M magnesium acetate and 18 % PEG3350 Ligands: 5 mM NADP+ and 50 mM 2-keto-hexanoic acid
Crystal Properties
Matthews coefficientSolvent content
2.6954.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.53α = 90
b = 87.4β = 96.34
c = 66.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9507DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.452.5195.50.03615.47.7132820
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4291.50.3772.486288

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5MH61.452.51125480667595.240.137460.135870.16701RANDOM20.538
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]
-0.880.1-0.311.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.918
r_sphericity_bonded27.574
r_sphericity_free26.866
r_dihedral_angle_4_deg19.89
r_rigid_bond_restr12.361
r_dihedral_angle_3_deg12.035
r_scbond_it9.528
r_scbond_other9.493
r_scangle_other8.963
r_long_range_B_refined7.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.918
r_sphericity_bonded27.574
r_sphericity_free26.866
r_dihedral_angle_4_deg19.89
r_rigid_bond_restr12.361
r_dihedral_angle_3_deg12.035
r_scbond_it9.528
r_scbond_other9.493
r_scangle_other8.963
r_long_range_B_refined7.947
r_long_range_B_other7.946
r_mcbond_it6.573
r_mcbond_other6.573
r_mcangle_it6.311
r_mcangle_other6.31
r_dihedral_angle_1_deg6.198
r_angle_refined_deg1.588
r_angle_other_deg1.315
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4698
Nucleic Acid Atoms
Solvent Atoms676
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
Cootmodel building