8JBZ

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Rhodococcus erythropolis SQ1 in complex with 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 DROP72911.8 M Ammonium citrate tribasic, pH7.0
Crystal Properties
Matthews coefficientSolvent content
4.572.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.108α = 90
b = 120.108β = 90
c = 117.242γ = 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)CC (Half)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
12.079104.234100116.210.558119
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.082.140.858

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.079104.23458114285099.9230.1960.19440.228641.679
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]
0.8130.4070.813-2.637
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.662
r_dihedral_angle_4_deg21.173
r_dihedral_angle_3_deg15.645
r_lrange_other7.884
r_lrange_it7.878
r_scangle_it7.735
r_scangle_other7.733
r_dihedral_angle_1_deg6.626
r_scbond_it5.801
r_scbond_other5.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.662
r_dihedral_angle_4_deg21.173
r_dihedral_angle_3_deg15.645
r_lrange_other7.884
r_lrange_it7.878
r_scangle_it7.735
r_scangle_other7.733
r_dihedral_angle_1_deg6.626
r_scbond_it5.801
r_scbond_other5.8
r_mcangle_it4.728
r_mcangle_other4.727
r_mcbond_it3.665
r_mcbond_other3.665
r_angle_other_deg2.442
r_angle_refined_deg1.762
r_nbd_other0.409
r_symmetry_nbd_refined0.391
r_symmetry_nbd_other0.218
r_nbd_refined0.214
r_nbtor_refined0.166
r_symmetry_xyhbond_nbd_refined0.148
r_xyhbond_nbd_refined0.122
r_chiral_restr0.079
r_symmetry_nbtor_other0.079
r_bond_other_d0.037
r_bond_refined_d0.012
r_gen_planes_other0.012
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3812
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms74

Software

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