3NUV | pdb_00003nuv

Crystal structure of ketosteroid isomerase D38ND99N 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
18.52981.8 M ammonium sulfate, 100 mM Tris-HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7855.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.785α = 90
b = 59.785β = 90
c = 144.499γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-03-25SINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 325 mm CCD2010-03-24SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2
2SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
1,21.75829.627990.09612.16.62952224.8
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)
1,21.7581.8593.70.011.0470.55.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 8CHO1.7629.62729405294051499990.1770.1760.180.1980.2RANDOM27.91
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]
0.860.86-1.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.089
r_dihedral_angle_4_deg19.797
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg6.828
r_scangle_it4.063
r_scbond_it2.758
r_angle_refined_deg1.826
r_mcangle_it1.675
r_mcbond_it0.998
r_chiral_restr0.106
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.089
r_dihedral_angle_4_deg19.797
r_dihedral_angle_3_deg16.4
r_dihedral_angle_1_deg6.828
r_scangle_it4.063
r_scbond_it2.758
r_angle_refined_deg1.826
r_mcangle_it1.675
r_mcbond_it0.998
r_chiral_restr0.106
r_bond_refined_d0.017
r_gen_planes_refined0.009
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 Atoms1882
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms66

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing