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Crystal structure of non-classical TS inhibitor 2 in complex with Toxoplasma gondii TS-DHFR
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, HANGING DROP 7.3 293 18% PEG 3350, 0.1 M Potassium Formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.539 α = 89.97 b = 145.122 β = 89.95 c = 176.159 γ = 89.89
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray PIXEL PSI PILATUS 6M 2012-11-04 M SINGLE WAVELENGTH 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.79 48.28 94.34 128608 121332 2 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4EIL 2.79 48.28 2 128608 121332 6475 97.77 0.2222 0.2222 0.2198 0.2209 0.2676 0.2637 RANDOM 79.025
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] -1.1 0.25 -3.58 -0.25 4.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.737 r_dihedral_angle_4_deg 20.301 r_dihedral_angle_3_deg 19.366 r_mcangle_it 7.641 r_dihedral_angle_1_deg 7.06 r_mcbond_it 5.164 r_mcbond_other 5.164 r_angle_refined_deg 1.636 r_angle_other_deg 0.961 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.737 r_dihedral_angle_4_deg 20.301 r_dihedral_angle_3_deg 19.366 r_mcangle_it 7.641 r_dihedral_angle_1_deg 7.06 r_mcbond_it 5.164 r_mcbond_other 5.164 r_angle_refined_deg 1.636 r_angle_other_deg 0.961 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 31444 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 976
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing