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2.4 Angstrom Resolution Crystal Structure of Putative Nucleoside Diphosphate Kinase from Toxoplasma gondii.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NDL PDB ENTRY 1NDL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3;
Screen: Classics II (F6), 0.2M Ammonium sulfate, 0.1M PIS-TRIS pH 5.5, 25% (w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.02 39.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.385 α = 90 b = 121.591 β = 90 c = 212.274 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD Beryllium lenses 2013-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.4 30 99.6 0.084 0.084 18.2 5.7 75092 75092 -3 51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 99.8 0.523 0.523 3.2 5.8 3725
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NDL 2.4 29.49 71019 71019 3771 99.53 0.19462 0.19462 0.19229 0.23791 0.2375 RANDOM 48.676
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] 1.2 0.34 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.305 r_dihedral_angle_4_deg 11.821 r_dihedral_angle_3_deg 9.267 r_long_range_B_refined 5.394 r_long_range_B_other 5.26 r_scangle_other 2.578 r_dihedral_angle_1_deg 2.505 r_mcangle_it 2.174 r_mcangle_other 2.174 r_scbond_it 1.685
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.305 r_dihedral_angle_4_deg 11.821 r_dihedral_angle_3_deg 9.267 r_long_range_B_refined 5.394 r_long_range_B_other 5.26 r_scangle_other 2.578 r_dihedral_angle_1_deg 2.505 r_mcangle_it 2.174 r_mcangle_other 2.174 r_scbond_it 1.685 r_scbond_other 1.587 r_mcbond_it 1.363 r_mcbond_other 1.362 r_angle_refined_deg 1.219 r_angle_other_deg 0.706 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14699 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 70
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling