3NBR

Crystal Structure of Ketosteroid Isomerase D38NP39GD99N from Pseudomonas Testosteroni (tKSI) with 4-Androstene-3,17-dione Bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8CHOPDB ENTRY 8CHO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.22982 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 2mM DTT, pH 7.2, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7955.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.168α = 90
b = 60.168β = 90
c = 142.585γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-14SINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 325 mm CCD2010-01-05SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.97946SSRLBL9-1
2SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1,21.7352.10799.90.05830.919.21674816748
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.731.8299.50.0232.2651.415.7

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 8CHO1.7352.107164071557783098.150.234110.232520.26483RANDOM43.128
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]
1.470.731.47-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.438
r_dihedral_angle_4_deg19.089
r_dihedral_angle_3_deg18.526
r_dihedral_angle_1_deg8.607
r_scangle_it5.308
r_scbond_it3.423
r_angle_refined_deg2.258
r_mcangle_it2.219
r_mcbond_it1.325
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.438
r_dihedral_angle_4_deg19.089
r_dihedral_angle_3_deg18.526
r_dihedral_angle_1_deg8.607
r_scangle_it5.308
r_scbond_it3.423
r_angle_refined_deg2.258
r_mcangle_it2.219
r_mcbond_it1.325
r_chiral_restr0.144
r_bond_refined_d0.026
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms934
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms36

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
Web-Icedata collection
XDSdata reduction