4KTL

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4,4'-(3-((4-hydroxyphenyl)amino)-1H-pyrazole-4,5-diyl)diphenol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1N40PDB entry 1N40

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP62772M Ammonium sulfate, 0.1M Sodium cacodylate-HCl, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.789α = 90
b = 77.789β = 90
c = 264.241γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCUSTOM-MADE2012-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.917310DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9553.5197.515.14346833468322
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0688.47.52.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 1N401.9538.8923289032890172897.20.1450.1430.189RANDOM15.62
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]
0.010.010.01-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.693
r_dihedral_angle_4_deg15.92
r_dihedral_angle_3_deg13.192
r_dihedral_angle_1_deg5.555
r_angle_refined_deg2.11
r_angle_other_deg1.805
r_chiral_restr0.136
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_gen_planes_other0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.693
r_dihedral_angle_4_deg15.92
r_dihedral_angle_3_deg13.192
r_dihedral_angle_1_deg5.555
r_angle_refined_deg2.11
r_angle_other_deg1.805
r_chiral_restr0.136
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_gen_planes_other0.009
r_bond_other_d0.002
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2984
Nucleic Acid Atoms
Solvent Atoms511
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing