3NM2

Crystal Structure of Ketosteroid Isomerase D38EP39GV40GS42G from Pseudomonas Testosteroni (tKSI)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72982.0 M ammonium sulfate, 20 mM potassium phosphate, 1 mM EDTA, 1 mM DTT, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7154.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.356α = 90
b = 59.356β = 90
c = 141.974γ = 120
Symmetry
Space GroupP 65 2 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 BL9-20.97946SSRLBL9-2
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
1,21.88729.67899.60.07821.613.2126141261429.1
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)
1,21.8871.9997.20.9830.9830.810.81741

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 8CHO1.88729.678125631256361099.530.20480.20480.20240.2536RANDOM37.019
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]
1.410.711.41-2.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.215
r_dihedral_angle_4_deg17.854
r_dihedral_angle_3_deg15.211
r_dihedral_angle_1_deg6.952
r_scangle_it6.085
r_scbond_it3.858
r_mcangle_it2.301
r_angle_refined_deg2.137
r_mcbond_it1.39
r_chiral_restr0.152
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.215
r_dihedral_angle_4_deg17.854
r_dihedral_angle_3_deg15.211
r_dihedral_angle_1_deg6.952
r_scangle_it6.085
r_scbond_it3.858
r_mcangle_it2.301
r_angle_refined_deg2.137
r_mcbond_it1.39
r_chiral_restr0.152
r_bond_refined_d0.026
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms938
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms30

Software

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