4APN

Structure of TR from Leishmania infantum in complex with a diarylpirrole-based inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JK6PDB ENTRY 2JK6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.1 M TRIS, 1.6 M AMMONIUM SULPHATE PH 8.5
Crystal Properties
Matthews coefficientSolvent content
4.674

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.561α = 90
b = 102.561β = 90
c = 191.985γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
13.2501000.1216.77.2327892
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)
13.23.311000.473.57.3

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2JK63.25030966165299.910.241070.239150.27676RANDOM73.108
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]
4.144.14-8.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_dihedral_angle_3_deg16.272
r_dihedral_angle_4_deg12.709
r_dihedral_angle_1_deg4.373
r_angle_refined_deg1.352
r_scangle_it0.566
r_mcangle_it0.502
r_scbond_it0.313
r_mcbond_it0.276
r_chiral_restr0.112
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.577
r_dihedral_angle_3_deg16.272
r_dihedral_angle_4_deg12.709
r_dihedral_angle_1_deg4.373
r_angle_refined_deg1.352
r_scangle_it0.566
r_mcangle_it0.502
r_scbond_it0.313
r_mcbond_it0.276
r_chiral_restr0.112
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
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_mcbond_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 Atoms7388
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms318

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing