3W8F

Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor malonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VDR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529332% PEG4000, 100mM Tris hydrochloride, 200mM malonate, 5mM NAD+, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1743.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.83α = 90
b = 62.83β = 90
c = 119.29γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.00Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
10.9922.9598.014226042260
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.53100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3VDR1.4520.824215441170418297.660.144780.142250.16735RANDOM9.655
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.212
r_dihedral_angle_3_deg12.96
r_dihedral_angle_4_deg9.303
r_dihedral_angle_1_deg6.186
r_scangle_it5.458
r_scbond_it3.301
r_angle_refined_deg2.367
r_mcangle_it2.104
r_mcbond_it1.281
r_chiral_restr0.148
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.212
r_dihedral_angle_3_deg12.96
r_dihedral_angle_4_deg9.303
r_dihedral_angle_1_deg6.186
r_scangle_it5.458
r_scbond_it3.301
r_angle_refined_deg2.367
r_mcangle_it2.104
r_mcbond_it1.281
r_chiral_restr0.148
r_bond_refined_d0.027
r_gen_planes_refined0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1906
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms53

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling