3T70

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72942.2M Ammonium sulphate, 0.2M di-sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.5150.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.75α = 90
b = 76.75β = 90
c = 105.83γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2009-05-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.980DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.843.561000.04812.57.45671156711
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.843.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1VYQ1.837.895671153806286299.980.200850.200850.19920.23225RANDOM28.139
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]
0.060.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.522
r_dihedral_angle_4_deg19.436
r_dihedral_angle_3_deg12.531
r_dihedral_angle_1_deg6.377
r_scangle_it2.254
r_scbond_it1.397
r_angle_refined_deg1.133
r_mcangle_it1.115
r_mcbond_it0.652
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.522
r_dihedral_angle_4_deg19.436
r_dihedral_angle_3_deg12.531
r_dihedral_angle_1_deg6.377
r_scangle_it2.254
r_scbond_it1.397
r_angle_refined_deg1.133
r_mcangle_it1.115
r_mcbond_it0.652
r_nbtor_refined0.305
r_symmetry_vdw_refined0.184
r_nbd_refined0.179
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.137
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 AtomsNumber
Protein Atoms3458
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms120

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling