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1.8 Angstrom resolution crystal structure of a putative deoxyribose-phosphate aldolase from Toxoplasma gondii ME49
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 277 Protein at 7 mg/mL in 10 mM Tris/HCl, pH=8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: 0.1 M Citric acid, pH=4.0, 0.8 M Ammonium sulfate (The AmSO4 suite, condition E1 (49)). Cryo condition: 1:1 v/v 50 % sucrose:E1 condition , VAPOR DIFFUSION, SITTING DROP, temperature 277 and 287K
Crystal Properties Matthews coefficient Solvent content 2.61 52.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.923 α = 62.9 b = 72.194 β = 89.8 c = 73.048 γ = 88.85
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 Be-Lenses/Diamond Laue Mono 2011-02-17 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) 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 1.8 30 97.6 0.063 14.66 3.1 116483 116483 -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 1.8 1.83 96.2 0.495 2.36 3.1
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 2A4A 1.8 29.49 110552 110552 5879 97.26 0.1674 0.16568 0.1765 0.2006 0.2112 RANDOM 32.566
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] 1.21 -0.87 1.07 1.22 -0.91 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.73 r_dihedral_angle_4_deg 8.177 r_dihedral_angle_3_deg 7.081 r_scangle_it 5.102 r_scbond_it 3.069 r_mcangle_it 1.896 r_dihedral_angle_1_deg 1.481 r_angle_refined_deg 1.464 r_mcbond_it 1.034 r_angle_other_deg 0.827
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.73 r_dihedral_angle_4_deg 8.177 r_dihedral_angle_3_deg 7.081 r_scangle_it 5.102 r_scbond_it 3.069 r_mcangle_it 1.896 r_dihedral_angle_1_deg 1.481 r_angle_refined_deg 1.464 r_mcbond_it 1.034 r_angle_other_deg 0.827 r_mcbond_other 0.298 r_chiral_restr 0.101 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8272 Nucleic Acid Atoms Solvent Atoms 927 Heterogen Atoms 149
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling