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X-ray crystal structure of Plasmodium vivax dihydrofolate reductase in complex with pyrimethamine and its derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J3J PDB ENTRY 1J3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 30%PEG4000, 100MM TRIS-HCL, PH 7.2, 10%GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.79 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.28 α = 90 b = 55.74 β = 107.09 c = 45.72 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE RIGAKU R-AXIS MIRRORS 2002-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.9 30.47 99.1 0.04 14.8 3.21 24170 2 32.3
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 1.9 1.97 99.1 0.41 3.3 3.19
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 1J3J 1.9 30.47 24170 2392 94.3 0.208 0.208 0.2086 0.26 0.2599 RANDOM 39.6
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] 7.29 -0.23 0.25 -7.54
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 4.97 c_scbond_it 4.17 c_mcangle_it 3.62 c_mcbond_it 2.83 c_angle_deg 1.5 c_improper_angle_d 0.97 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.5 c_scangle_it 4.97 c_scbond_it 4.17 c_mcangle_it 3.62 c_mcbond_it 2.83 c_angle_deg 1.5 c_improper_angle_d 0.97 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1762 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 65
Software Software Software Name Purpose CNS refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing