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Crystal structure of the C258S/C268S variant of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) in complex with magnesium and AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A57 PDB ENTRY 4A57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 MM KCL, 10 MM MGCL2, 50 MM TRIS PH 8.5, 30% PEG 400, 2 MM AMPPNP AND 10 MM MAGNESIUM ACETATE.
Crystal Properties Matthews coefficient Solvent content 2.48 50.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.953 α = 90 b = 150.668 β = 90 c = 486.988 γ = 90
Symmetry Space Group C 2 2 21
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.85 39 98.3 0.17 5 3.7 61587 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 3 94.3 0.45 5 3.4
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 PDB ENTRY 4A57 2.85 40 58171 3124 97.75 0.23627 0.23369 0.2331 0.28411 0.2839 RANDOM 36.962
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] 2.33 -0.57 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.777 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 16.759 r_dihedral_angle_1_deg 5.587 r_angle_refined_deg 1.45 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.777 r_dihedral_angle_4_deg 22.279 r_dihedral_angle_3_deg 16.759 r_dihedral_angle_1_deg 5.587 r_angle_refined_deg 1.45 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_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 Atoms Number Protein Atoms 18292 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing