4KTF

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4,4'-(3-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
2.6954.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.2α = 90
b = 78.2β = 90
c = 263.191γ = 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
11.3536.8292.65.92.9961289612822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.4296.32.3314436

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1N401.3535.71229130791307405291.350.167680.166270.19473RANDOM12.715
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.452
r_dihedral_angle_4_deg14.536
r_dihedral_angle_3_deg12.095
r_dihedral_angle_1_deg5.815
r_angle_refined_deg2.648
r_angle_other_deg1.719
r_chiral_restr0.166
r_bond_refined_d0.03
r_gen_planes_refined0.015
r_gen_planes_other0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.452
r_dihedral_angle_4_deg14.536
r_dihedral_angle_3_deg12.095
r_dihedral_angle_1_deg5.815
r_angle_refined_deg2.648
r_angle_other_deg1.719
r_chiral_restr0.166
r_bond_refined_d0.03
r_gen_planes_refined0.015
r_gen_planes_other0.011
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2979
Nucleic Acid Atoms
Solvent Atoms588
Heterogen Atoms83

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing