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Co-crystal structure of dihydrofolate reductase-thymidylate synthase from Babesia bovis with dUMP, Raltitrexed and NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K2H PDB ENTRY 3K2H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 1:1 CO-CRYSTALLIZATION DROP. PROTEIN SOLUTION: 20 MG/ML PROTEIN, 2.0MM DUMP, 2.0MM NADP, 5.0MM RALTITREXED, 0.5M SODIUM CHLORIDE, 0.025M HEPES, 5%(V/V) GLYCEROL, 2.0MM DITHIOTHREITOL. CRYSTALLANT SOLUTION (HT INDEX E11): 0.02M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1M HEPES, 22%(W/V) POLY(ACRYLIC ACID) SODIUM SALT 5100, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.33 α = 119.61 b = 83.83 β = 102.04 c = 83.92 γ = 90.26
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 315 2010-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.99740 ALS 5.0.1
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 1.8 50 97.2 0.06 12.3 2 108796
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 1.8 1.83 95.9 0.354 2.439 2 10489
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 3K2H 1.8 19.94 108796 104245 5573 98.52 0.1956 0.1935 0.2089 0.236 0.2515 RANDOM 19.8103
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] -1.91 0.06 -0.25 1.5 1.26 1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.942 r_dihedral_angle_4_deg 20.686 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 6.392 r_scangle_it 3.202 r_scbond_it 2.129 r_angle_refined_deg 1.753 r_mcangle_it 1.291 r_angle_other_deg 0.982 r_mcbond_it 0.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.942 r_dihedral_angle_4_deg 20.686 r_dihedral_angle_3_deg 12.993 r_dihedral_angle_1_deg 6.392 r_scangle_it 3.202 r_scbond_it 2.129 r_angle_refined_deg 1.753 r_mcangle_it 1.291 r_angle_other_deg 0.982 r_mcbond_it 0.758 r_mcbond_other 0.246 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7965 Nucleic Acid Atoms Solvent Atoms 1025 Heterogen Atoms 329
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection PHASES phasing