4QCK

Crystal structure of 3-ketosteroid-9-alpha-hydroxylase (KshA) from M. tuberculosis in complex with 4-androstene-3,17-dione


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5294500 mM NaH2PO4, 125 mM K2HPO4, 4% PEG- 1000, 20 mM Tris, 100 mM phosphate-citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.5365.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.8α = 90
b = 115.8β = 90
c = 80.81γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HEmirrors2012-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.92CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.4647.0661000.15313.7722383723062-350.347
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.5299.90.0181.61

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.4647.0722383723062115499.950.17990.1770.2353RANDOM47.076
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]
-0.65-0.32-0.652.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.472
r_dihedral_angle_4_deg15.818
r_dihedral_angle_3_deg13.527
r_dihedral_angle_1_deg6.457
r_mcangle_it5.944
r_mcbond_it4.213
r_mcbond_other4.205
r_angle_refined_deg1.264
r_angle_other_deg0.715
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.472
r_dihedral_angle_4_deg15.818
r_dihedral_angle_3_deg13.527
r_dihedral_angle_1_deg6.457
r_mcangle_it5.944
r_mcbond_it4.213
r_mcbond_other4.205
r_angle_refined_deg1.264
r_angle_other_deg0.715
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2900
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms31

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction