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Crystal structure of F16BP Aldolase from Toxoplasma gondii (TgALD1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KX6 PDB ENTRY 3KX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M SODIUM CHLORIDE, 0.1 M HEPES PH 7.5, 1.6 M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.814 α = 90 b = 109.814 β = 90 c = 54.357 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.75 50 99.4 0.05 44 13.5 33917 2
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 1.75 1.78 100 0.5 4 13.4
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 PDB ENTRY 3KX6 1.75 36.44 32144 1718 99.39 0.19218 0.19014 0.1962 0.23073 0.2384 RANDOM 31.612
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.414 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 15.666 r_dihedral_angle_1_deg 6.511 r_mcangle_it 3.719 r_scbond_it 3.593 r_mcbond_it 2.97 r_mcbond_other 2.937 r_angle_refined_deg 1.358 r_angle_other_deg 0.703
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.414 r_dihedral_angle_4_deg 17.026 r_dihedral_angle_3_deg 15.666 r_dihedral_angle_1_deg 6.511 r_mcangle_it 3.719 r_scbond_it 3.593 r_mcbond_it 2.97 r_mcbond_other 2.937 r_angle_refined_deg 1.358 r_angle_other_deg 0.703 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2563 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing