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5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYQ PDB ENTRY 1VYQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 2.2M Ammonium sulphate, 0.2M di-sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.53 51.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.01 α = 90 b = 77.01 β = 90 c = 106.28 γ = 90
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 MARMOSAIC 225 mm CCD mirrors 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.072 ESRF ID23-1
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 1.65 36.2 100 0.082 11.5 5.5 74358 74358
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 36.2 100
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 (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 1VYQ 1.65 34.44 74358 70573 3739 99.98 0.1914 0.1914 0.19014 0.1876 0.21555 0.2127 RANDOM 23.562
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.473 r_dihedral_angle_4_deg 18.959 r_dihedral_angle_3_deg 12.872 r_dihedral_angle_1_deg 6.811 r_scangle_it 3.618 r_scbond_it 2.225 r_mcangle_it 1.534 r_angle_refined_deg 1.335 r_mcbond_it 0.811 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.473 r_dihedral_angle_4_deg 18.959 r_dihedral_angle_3_deg 12.872 r_dihedral_angle_1_deg 6.811 r_scangle_it 3.618 r_scbond_it 2.225 r_mcangle_it 1.534 r_angle_refined_deg 1.335 r_mcbond_it 0.811 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3511 Nucleic Acid Atoms Solvent Atoms 322 Heterogen Atoms 107
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling