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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 4.8 294 0.2M ammonium sulphate, 0.1M sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.55 51.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.972 α = 90 b = 76.972 β = 90 c = 106.924 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 2005-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 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 2.396 40 99.3 0.09 13.6 3.9 24538 24538
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 2.396 40 24538 23083 1244 99.3 0.19905 0.19905 0.19618 0.1939 0.2536 0.2528 RANDOM 34.671
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] -0.55 -0.55 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.797 r_dihedral_angle_3_deg 18.297 r_dihedral_angle_4_deg 16.925 r_dihedral_angle_1_deg 8.592 r_scangle_it 4.492 r_scbond_it 3.069 r_angle_refined_deg 2.508 r_mcangle_it 2.012 r_mcbond_it 1.168 r_chiral_restr 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.797 r_dihedral_angle_3_deg 18.297 r_dihedral_angle_4_deg 16.925 r_dihedral_angle_1_deg 8.592 r_scangle_it 4.492 r_scbond_it 3.069 r_angle_refined_deg 2.508 r_mcangle_it 2.012 r_mcbond_it 1.168 r_chiral_restr 0.43 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.186 r_xyhbond_nbd_refined 0.174 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 3323 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 123
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling