2WDZ

Crystal structure of the short chain dehydrogenase Galactitol- Dehydrogenase (GatDH) of Rhodobacter sphaeroides in complex with NAD+ and 1,2-Pentandiol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5100MM MES PH 5.5, 200MM MAGNESIUM CHLORIDE, 12.5%(W/V)MPEG5000
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.72α = 90
b = 113.62β = 90
c = 256.925γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORSMSINGLE 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)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
11.952098.50.12715.18.9640191.823.51
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)
11.952.0694.90.6911.84.8

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 REPLACEMENTTHROUGHOUTSWISS PROT MODEL1.9519.8660703324098.380.1890.1870.24RANDOM27.368
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.156
r_dihedral_angle_4_deg19.792
r_dihedral_angle_3_deg15.447
r_dihedral_angle_1_deg6.141
r_angle_refined_deg1.69
r_angle_other_deg1.199
r_symmetry_hbond_refined0.779
r_symmetry_vdw_other0.282
r_nbd_other0.21
r_nbd_refined0.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.156
r_dihedral_angle_4_deg19.792
r_dihedral_angle_3_deg15.447
r_dihedral_angle_1_deg6.141
r_angle_refined_deg1.69
r_angle_other_deg1.199
r_symmetry_hbond_refined0.779
r_symmetry_vdw_other0.282
r_nbd_other0.21
r_nbd_refined0.205
r_symmetry_vdw_refined0.204
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.168
r_chiral_restr0.104
r_nbtor_other0.092
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7386
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing