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Co-crystal structure of dihydrofolate reductase/thymidylate synthase from Babesia bovis with dUMP, Pemetrexed and NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I3R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 289 11.3 mg/mL BaboA.01191.a, 2 mM dUMP, 2 mM Pemetrexed, NADP carried through from protein purification so it could be NADP or NADPH; soak of apo crystals grown in 20% PEG 8000, 0.1 M CHES pH 9.5; crystal tracking ID 204850f1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.56 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.144 α = 119.69 b = 83.196 β = 90.85 c = 83.378 γ = 101.71
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 RIGAKU SATURN 944+ 2009-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.2 50 98.5 0.096 15.4 4 58064
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 2.2 2.24 82.6 0.286 3.16 2.7 2401
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 3i3r 2.2 35.2 57443 2917 97.03 0.192 0.19 0.2042 0.239 0.2512 RANDOM 16.674
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] 1.4 0.6 0.21 -0.06 0.78 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 21.604 r_dihedral_angle_3_deg 14.171 r_dihedral_angle_1_deg 6.556 r_scangle_it 2.851 r_scbond_it 1.933 r_angle_refined_deg 1.507 r_mcangle_it 1.17 r_mcbond_it 0.654 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.686 r_dihedral_angle_4_deg 21.604 r_dihedral_angle_3_deg 14.171 r_dihedral_angle_1_deg 6.556 r_scangle_it 2.851 r_scbond_it 1.933 r_angle_refined_deg 1.507 r_mcangle_it 1.17 r_mcbond_it 0.654 r_chiral_restr 0.109 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8001 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 280
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling