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1.7 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii with Tyrosine of Tag Bound to Active Site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 Protein:7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3;
Screen: PACT (B10), 0.2 M Magnesium chloride, 0.1 M MES pH 6.0, 20% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.814 α = 90 b = 73.4 β = 116.83 c = 122.671 γ = 90
Symmetry Space Group C 1 2 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 300 mm CCD 2015-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97890 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 30 98.5 0.059 0.059 22 4.9 202729 202729 -3 28
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 1.7 1.73 99.9 0.482 3.2 4.9
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 4O0N 1.7 29.98 192440 10203 98.23 0.15551 0.15361 0.1624 0.1917 0.1962 RANDOM 33.435
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] -0.66 0.04 1.74 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.188 r_dihedral_angle_4_deg 16.653 r_dihedral_angle_3_deg 10.952 r_long_range_B_refined 6.765 r_long_range_B_other 6.765 r_dihedral_angle_1_deg 3.858 r_scangle_other 3.38 r_scbond_it 2.258 r_scbond_other 2.256 r_mcangle_it 2.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.188 r_dihedral_angle_4_deg 16.653 r_dihedral_angle_3_deg 10.952 r_long_range_B_refined 6.765 r_long_range_B_other 6.765 r_dihedral_angle_1_deg 3.858 r_scangle_other 3.38 r_scbond_it 2.258 r_scbond_other 2.256 r_mcangle_it 2.218 r_mcangle_other 2.218 r_mcbond_it 1.499 r_mcbond_other 1.499 r_angle_refined_deg 1.398 r_angle_other_deg 0.79 r_chiral_restr 0.092 r_gen_planes_refined 0.022 r_gen_planes_other 0.017 r_bond_refined_d 0.01 r_bond_other_d 0.001 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 14647 Nucleic Acid Atoms Solvent Atoms 1854 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling BLU-MAX data collection PHASER phasing