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Crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) in complex with AMP
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 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.17 α = 90 b = 166.03 β = 97.15 c = 97.94 γ = 90
Symmetry Space Group P 1 21 1
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.2 43.4 96.9 0.08 7.6 3 142618 2.9 37.3
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 2.2 2.3 93.3 0.08 2 2.9
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 2.2 42.3 142579 1399 0.1802 0.1797 0.1892 0.2277 0.2382 RANDOM 41.42
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] 1.617 2.5628 -2.4929 0.8758
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.53 t_omega_torsion 3 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.53 t_omega_torsion 3 t_angle_deg 1.14 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18381 Nucleic Acid Atoms Solvent Atoms 884 Heterogen Atoms 115
Software Software Software Name Purpose BUSTER refinement MOSFLM data reduction SCALA data scaling MOLREP phasing