3I65

Plasmodium falciparum dihydroorotate dehydrogenase bound with triazolopyrimidine-based inhibitor DSM1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TV5PDB ENTRY 1TV5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62930.16 M Ammonium sulfate, 0.1 M Sodium Acetate, pH 4.6, 18-20% PEG4000, 25% Glycerol, and 10 mM DTT, EVAPORATION, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
3.1661.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.858α = 90
b = 85.858β = 90
c = 138.352γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315high-resolution double-crystal monochromator2008-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.00APS19-ID

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
125091.50.058451245761421941.91.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.06680.5151.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1TV52501.5413203775480291.370.21260.21220.21220.24807RANDOM45.511
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]
1.220.611.22-1.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.658
r_dihedral_angle_4_deg21.719
r_dihedral_angle_3_deg15.24
r_dihedral_angle_1_deg6.367
r_scangle_it2.728
r_scbond_it1.747
r_mcangle_it1.383
r_angle_refined_deg1.308
r_mcbond_it0.816
r_symmetry_vdw_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.658
r_dihedral_angle_4_deg21.719
r_dihedral_angle_3_deg15.24
r_dihedral_angle_1_deg6.367
r_scangle_it2.728
r_scbond_it1.747
r_mcangle_it1.383
r_angle_refined_deg1.308
r_mcbond_it0.816
r_symmetry_vdw_refined0.322
r_nbtor_refined0.309
r_nbd_refined0.209
r_xyhbond_nbd_refined0.131
r_chiral_restr0.095
r_symmetry_hbond_refined0.081
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2934
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms79

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling