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Crystal structure of the Toxoplasma gondii Pyruvate Kinase N terminal truncated
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EOE PDB entry 3EOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 5 % PEG 3350, 0.1 M Succinic Acid, pH 7.0, 3 mM Chembridge #5175181, 20% glycerol, Vapor diffusion, hanging drop
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.023 α = 90 b = 92.311 β = 105.57 c = 112.443 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 IMAGE PLATE RIGAKU RAXIS IV++ 2008-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
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 2.2 50 97.9 0.088 0.053 3.8 108075 105806
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 2.2 2.28 96.3 0.913 0.913 2 3.8
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 (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 3EOE 2.21 42.45 108075 100484 5263 97.61 0.20923 0.20634 0.2327 0.26516 0.2826 RANDOM 35.302
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] 1.94 2.35 0.11 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.129 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 17.413 r_dihedral_angle_1_deg 5.462 r_scangle_it 2.111 r_scbond_it 1.312 r_angle_refined_deg 1.282 r_mcangle_it 0.701 r_mcbond_it 0.435 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.129 r_dihedral_angle_4_deg 18.235 r_dihedral_angle_3_deg 17.413 r_dihedral_angle_1_deg 5.462 r_scangle_it 2.111 r_scbond_it 1.312 r_angle_refined_deg 1.282 r_mcangle_it 0.701 r_mcbond_it 0.435 r_nbtor_refined 0.296 r_symmetry_hbond_refined 0.213 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14240 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 16
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction