3LQF

Crystal structure of the short-chain dehydrogenase Galactitol-Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD and erythritol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModelSWISS PROT MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.7291100MM MES, 200MM MAGNESIUMCHLORIDE, 14.0%(W/V)MPEG5000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1241.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.863α = 90
b = 113.838β = 90
c = 123.234γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIXMIRRORS2008-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.2BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.83099.90.0780.07817.657.3838228382228.474
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.81.8599.30.680.682.966.86087

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSWISS PROT MODEL1.830796317963141911000.18610.18610.184190.22267RANDOM24.924
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]
-0.492.36-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.583
r_dihedral_angle_4_deg17.487
r_dihedral_angle_3_deg15.112
r_dihedral_angle_1_deg5.96
r_scangle_it3.24
r_scbond_it2.062
r_angle_refined_deg1.389
r_mcangle_it1.331
r_mcbond_it0.787
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.583
r_dihedral_angle_4_deg17.487
r_dihedral_angle_3_deg15.112
r_dihedral_angle_1_deg5.96
r_scangle_it3.24
r_scbond_it2.062
r_angle_refined_deg1.389
r_mcangle_it1.331
r_mcbond_it0.787
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7392
Nucleic Acid Atoms
Solvent Atoms509
Heterogen Atoms210

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling