☰ Navigation Tabs
Crystal structure of Toxoplasma gondii TS-DHFR complexed with NADPH, dUMP, PDDF, and 5-(4-(3-(2-methoxypyrimidin-5-yl)phenyl)piperazin-1-yl)pyrimidine-2,4-diamine (TRC-2533)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EIL PDB entry 4EIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 0.2 M ammonium citrate, pH 4.6, 15% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.209 α = 90 b = 144.343 β = 90 c = 174.189 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 ADSC QUANTUM 315r 2016-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979282 SSRF BL17U1
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 3.5 50 62.7 0.138 12 4.7 11564
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 3.5 3.63 0.523
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4EIL 3.5 50 10949 556 62.06 0.20148 0.19833 0.26437 0.2658 RANDOM 50.492
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] -0.99 -0.3 1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.711 r_dihedral_angle_3_deg 17.987 r_dihedral_angle_4_deg 16.097 r_long_range_B_refined 7.193 r_dihedral_angle_1_deg 5.558 r_mcangle_it 2.547 r_mcbond_it 1.399 r_angle_refined_deg 1.118 r_scbond_it 0.975 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.711 r_dihedral_angle_3_deg 17.987 r_dihedral_angle_4_deg 16.097 r_long_range_B_refined 7.193 r_dihedral_angle_1_deg 5.558 r_mcangle_it 2.547 r_mcbond_it 1.399 r_angle_refined_deg 1.118 r_scbond_it 0.975 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 8172 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 262
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing HKL-2000 data extraction Blu-Ice data collection HKL-2000 data processing