2WSB

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.54% N-PROPANOLE, 100MM SODIUM CACODYLATE, PH 6.5, 200MM SODIUM ACETATE, 30% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.7155

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.79α = 90
b = 106.62β = 90
c = 109.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.2519.9498.60.18.46.7313700220.5
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)
11.251.2892.90.5622.5

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 MODEL1.2519.943133201566699.880.136090.133930.17749RANDOM21.51
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]
0.09-0.06-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_sphericity_free21.107
r_dihedral_angle_4_deg18.654
r_dihedral_angle_3_deg12.454
r_sphericity_bonded9.851
r_scangle_it8.378
r_scbond_it6.863
r_dihedral_angle_1_deg6.314
r_mcangle_it4.112
r_mcbond_it3.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_sphericity_free21.107
r_dihedral_angle_4_deg18.654
r_dihedral_angle_3_deg12.454
r_sphericity_bonded9.851
r_scangle_it8.378
r_scbond_it6.863
r_dihedral_angle_1_deg6.314
r_mcangle_it4.112
r_mcbond_it3.1
r_rigid_bond_restr3.07
r_angle_refined_deg2.581
r_symmetry_vdw_refined0.264
r_symmetry_hbond_refined0.254
r_chiral_restr0.168
r_bond_refined_d0.03
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7392
Nucleic Acid Atoms
Solvent Atoms1765
Heterogen Atoms210

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing