7P18

Crystal structure of 3-ketosteroid delta1-dehydrogenase from Sterolibacterium denitrificans 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 DROP7.52770.1 M HEPES pH 7.5, 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7655.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.369α = 90
b = 130.369β = 90
c = 139.742γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-01-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.8447.7199.520.1130.1290.070.0570.9791.66.911908529.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.841.8998.70.7190.4860.7530.5156.7

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 REPLACEMENTTHROUGHOUT4C3Y1.8447.71116410210099.520.185140.184610.21401RANDOM35.846
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]
0.50.250.5-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.027
r_dihedral_angle_4_deg16.695
r_dihedral_angle_3_deg12.34
r_long_range_B_refined7.377
r_long_range_B_other7.289
r_dihedral_angle_1_deg7.031
r_scangle_other5.373
r_mcangle_it4.242
r_mcangle_other4.242
r_scbond_it3.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.027
r_dihedral_angle_4_deg16.695
r_dihedral_angle_3_deg12.34
r_long_range_B_refined7.377
r_long_range_B_other7.289
r_dihedral_angle_1_deg7.031
r_scangle_other5.373
r_mcangle_it4.242
r_mcangle_other4.242
r_scbond_it3.669
r_scbond_other3.668
r_mcbond_it3.17
r_mcbond_other3.168
r_angle_refined_deg1.523
r_angle_other_deg1.367
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms8567
Nucleic Acid Atoms
Solvent Atoms826
Heterogen Atoms181

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
XDSdata scaling
PHASERphasing