5LI6

Crystal structure of Mycobacterium tuberculosis CYP126A1 in complex with N-isopropyl-N-((3-(4-methoxyphenyl)-1,2,4-oxadiazol-5-yl)methyl)-2-(4-nitrophenyl)acetamide


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M carboxylic acids, 0.1M imidazole-MES pH 6.5, 30% PEG 8K
Crystal Properties
Matthews coefficientSolvent content
2.6553.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.62α = 90
b = 59.66β = 98.03
c = 118.47γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2011-01-19MSINGLE 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
11.9532.1499.50.03111.9466993
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)
11.951.9996.80.8421.83.4

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 REPLACEMENTTHROUGHOUT1OXA1.9532.146699335601000.188510.185680.24174RANDOM16.965
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]
0.980.19-0.5-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.83
r_dihedral_angle_4_deg16.744
r_dihedral_angle_3_deg13.892
r_dihedral_angle_1_deg5.842
r_scangle_it4.703
r_scbond_it3.035
r_mcangle_it1.81
r_angle_refined_deg1.775
r_mcbond_it1.037
r_angle_other_deg1.034
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.83
r_dihedral_angle_4_deg16.744
r_dihedral_angle_3_deg13.892
r_dihedral_angle_1_deg5.842
r_scangle_it4.703
r_scbond_it3.035
r_mcangle_it1.81
r_angle_refined_deg1.775
r_mcbond_it1.037
r_angle_other_deg1.034
r_mcbond_other0.305
r_chiral_restr0.114
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms5930
Nucleic Acid Atoms
Solvent Atoms872
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling