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1.37 Angstrom resolution crystal structure of apo-form 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 3QYQ PDB entry 3QYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 The PACT suite B7(#19)-0.2 M NaCl, 0.1 M MES pH 6.0, 20% (w/v) PEG 6k. Protein at 12.7 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.97 37.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.982 α = 90 b = 73.284 β = 90 c = 96.378 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 300 mm CCD Be-Lenses 2012-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.37 30 99.4 0.047 27.99 6.7 107282 107282 -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 1.37 1.39 100 0.602 2.86 6.7
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 3QYQ 1.37 29.42 101562 101562 5325 99.41 0.15327 0.15158 0.1612 0.18485 0.1919 RANDOM 34.3
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] 2.09 -1.52 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.01 r_dihedral_angle_4_deg 11.221 r_dihedral_angle_3_deg 9.387 r_scangle_it 4.393 r_dihedral_angle_1_deg 4.002 r_scbond_it 2.975 r_mcangle_it 1.847 r_angle_refined_deg 1.428 r_mcbond_it 1.181 r_rigid_bond_restr 1.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.01 r_dihedral_angle_4_deg 11.221 r_dihedral_angle_3_deg 9.387 r_scangle_it 4.393 r_dihedral_angle_1_deg 4.002 r_scbond_it 2.975 r_mcangle_it 1.847 r_angle_refined_deg 1.428 r_mcbond_it 1.181 r_rigid_bond_restr 1.136 r_angle_other_deg 0.903 r_mcbond_other 0.381 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3883 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 12
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling