5GO1

Structural, Functional characterization and discovery of novel inhibitors of Leishmania amazonensis Nucleoside Diphosphatase Kinase (NDK)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293PEG MME 500, Bis-Tris Propane, Magnesium chloride, 30% ethylene glycol used as cryoprotectant
Crystal Properties
Matthews coefficientSolvent content
3.3162.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.18α = 90
b = 115.18β = 90
c = 62.18γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDbent collimating mirror and toroid2012-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.954ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
12.599.7598.40.0720.0750.9919.813.8862165.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6495.20.790.7682.310.1

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 REPLACEMENTTHROUGHOUT3NGR2.599.75820140797.290.227070.225250.2655RANDOM72.575
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]
1.440.721.44-4.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.973
r_dihedral_angle_3_deg20.167
r_dihedral_angle_4_deg18.905
r_long_range_B_other16.561
r_long_range_B_refined16.554
r_mcangle_it12.17
r_mcangle_other12.159
r_scangle_other10.762
r_mcbond_it8.423
r_mcbond_other8.411
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.973
r_dihedral_angle_3_deg20.167
r_dihedral_angle_4_deg18.905
r_long_range_B_other16.561
r_long_range_B_refined16.554
r_mcangle_it12.17
r_mcangle_other12.159
r_scangle_other10.762
r_mcbond_it8.423
r_mcbond_other8.411
r_dihedral_angle_1_deg7.423
r_scbond_it7.062
r_scbond_other7.062
r_angle_refined_deg1.992
r_angle_other_deg1.172
r_chiral_restr0.124
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms814
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing