2DKN

Crystal structure of the 3-alpha-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831 complexed with NADH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FK8PDB ENTRY 1FK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92770.1M Tris/HCl (pH 9.0), 0.14M sodium chloride, 1.4M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1442.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.457α = 90
b = 82.248β = 90
c = 86.569γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL38B11.000SPring-8BL38B1

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
11.82099.50.16824.567.38417764177615.2
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)
11.81.998.70.2495.87.15826

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1FK81.8204177639665211199.490.1860.173840.172190.2053RANDOM13.703
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]
0.34-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg20.082
r_dihedral_angle_3_deg14.74
r_dihedral_angle_1_deg10.381
r_scangle_it2.52
r_mcangle_it1.822
r_scbond_it1.633
r_angle_refined_deg1.472
r_mcbond_it1.203
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg20.082
r_dihedral_angle_3_deg14.74
r_dihedral_angle_1_deg10.381
r_scangle_it2.52
r_mcangle_it1.822
r_scbond_it1.633
r_angle_refined_deg1.472
r_mcbond_it1.203
r_nbtor_refined0.311
r_symmetry_hbond_refined0.263
r_symmetry_vdw_refined0.248
r_nbd_refined0.217
r_xyhbond_nbd_refined0.196
r_chiral_restr0.108
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3406
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing