8KCZ

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 1,4-androstadiene-3,17- dione


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C3Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289.150.2 M Lithium sulfate monohydrate, 0.1M BIS-TRIS ph 6.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
4.4372.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.89α = 90
b = 118.89β = 90
c = 118.61γ = 120
Symmetry
Space GroupP 31 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-01-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

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
12.3102.9699.70.01919.320.742673
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)
12.342.471.292

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTFREE R-VALUE2.329.740509216499.920.193240.191660.22291RANDOM53.403
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]
1.170.591.17-3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.846
r_dihedral_angle_4_deg21.129
r_dihedral_angle_3_deg16.741
r_long_range_B_refined13.369
r_long_range_B_other13.368
r_scangle_other9.033
r_dihedral_angle_1_deg6.874
r_scbond_it6.623
r_scbond_other6.622
r_mcangle_it5.975
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.846
r_dihedral_angle_4_deg21.129
r_dihedral_angle_3_deg16.741
r_long_range_B_refined13.369
r_long_range_B_other13.368
r_scangle_other9.033
r_dihedral_angle_1_deg6.874
r_scbond_it6.623
r_scbond_other6.622
r_mcangle_it5.975
r_mcangle_other5.974
r_mcbond_it4.688
r_mcbond_other4.669
r_angle_other_deg2.459
r_angle_refined_deg1.716
r_chiral_restr0.093
r_bond_other_d0.037
r_gen_planes_other0.012
r_bond_refined_d0.01
r_gen_planes_refined0.009
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_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3842
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms74

Software

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