5LI8

Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with ketoconazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OXA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2772 M sodium sulphate, 0.1 M Tris, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.23α = 90
b = 59.66β = 93.21
c = 69.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2010-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976DiamondI03

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
11.8343.8692.470.04819.13.937754
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)
11.831.8859.10.6662.23.3

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 REPLACEMENTTHROUGHOUT1OXA1.8343.863775319961000.157360.155250.19603RANDOM13.966
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]
0.110.420.03-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.138
r_dihedral_angle_4_deg19.381
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg5.534
r_scangle_it5.471
r_scbond_it3.476
r_mcangle_it2.122
r_angle_refined_deg2.001
r_mcbond_it1.232
r_angle_other_deg1.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.138
r_dihedral_angle_4_deg19.381
r_dihedral_angle_3_deg12.256
r_dihedral_angle_1_deg5.534
r_scangle_it5.471
r_scbond_it3.476
r_mcangle_it2.122
r_angle_refined_deg2.001
r_mcbond_it1.232
r_angle_other_deg1.082
r_mcbond_other0.413
r_chiral_restr0.127
r_bond_refined_d0.025
r_gen_planes_refined0.003
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3032
Nucleic Acid Atoms
Solvent Atoms484
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling