4AT2

The crystal structure of 3-ketosteroid-delta4-(5alpha)-dehydrogenase from Rhodococcus jostii RHA1 in complex with 4-androstene-3,17- dione


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6CRYSTALS WERE OBTAINED FROM 200 MM AMMONIUM ACETATE, 100 MM SODIUM CITRATE PH 5.6 AND 30%(W/V) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
3.1260.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.778α = 90
b = 116.082β = 90
c = 110.151γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.651.3595.20.1110.54.888007213.2
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)
11.61.6974.10.373.24.28

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.651.36780066401895.020.160.15930.1806RANDOM12.916
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]
0.4180.173-0.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.782
r_dihedral_angle_4_deg12.977
r_dihedral_angle_3_deg11.469
r_scangle_it5.246
r_dihedral_angle_1_deg5.179
r_scbond_it2.51
r_angle_refined_deg1.251
r_mcangle_it1.183
r_mcbond_it0.701
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.782
r_dihedral_angle_4_deg12.977
r_dihedral_angle_3_deg11.469
r_scangle_it5.246
r_dihedral_angle_1_deg5.179
r_scbond_it2.51
r_angle_refined_deg1.251
r_mcangle_it1.183
r_mcbond_it0.701
r_nbtor_refined0.305
r_symmetry_vdw_refined0.236
r_nbd_refined0.212
r_symmetry_hbond_refined0.101
r_xyhbond_nbd_refined0.09
r_chiral_restr0.086
r_bond_refined_d0.007
r_gen_planes_refined0.006
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_mcangle_other
r_scbond_other
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 Atoms3598
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms75

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling