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Structural, Functional characterization and discovery of novel inhibitors of Leishmania amazonensis Nucleoside Diphosphatase Kinase (NDK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NGR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG MME 500, Bis-Tris Propane, Magnesium chloride,
30% ethylene glycol used as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 3.31 62.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.18 α = 90 b = 115.18 β = 90 c = 62.18 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD bent collimating mirror and toroid 2012-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.954 ESRF BM14
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 99.75 98.4 0.072 0.075 0.99 19.8 13.8 8621 65.4
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) Redundancy Number Unique Reflections (All) 1 2.5 2.64 95.2 0.79 0.768 2.3 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3NGR 2.5 99.75 8201 407 97.29 0.22707 0.22525 0.2334 0.2655 0.264 RANDOM 72.575
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] 1.44 0.72 1.44 -4.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.973 r_dihedral_angle_3_deg 20.167 r_dihedral_angle_4_deg 18.905 r_long_range_B_other 16.561 r_long_range_B_refined 16.554 r_mcangle_it 12.17 r_mcangle_other 12.159 r_scangle_other 10.762 r_mcbond_it 8.423 r_mcbond_other 8.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.973 r_dihedral_angle_3_deg 20.167 r_dihedral_angle_4_deg 18.905 r_long_range_B_other 16.561 r_long_range_B_refined 16.554 r_mcangle_it 12.17 r_mcangle_other 12.159 r_scangle_other 10.762 r_mcbond_it 8.423 r_mcbond_other 8.411 r_dihedral_angle_1_deg 7.423 r_scbond_it 7.062 r_scbond_other 7.062 r_angle_refined_deg 1.992 r_angle_other_deg 1.172 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 814 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing