7WYF

Plasmodium falciparum dihydroorotate dehydrogenase (DHODH) in complex with its inhibitor 50


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RX0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M Tris-HCl (pH 7.5-9.5), 35 % (w/v) PEG 4000, 50 mM sodium formate
Crystal Properties
Matthews coefficientSolvent content
1.935.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.71α = 90
b = 71.77β = 90
c = 179.43γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97852SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.354.9499.60.9929.65.95898
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.33.480.5370.5870.892

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4RX03.345.99560229599.490.26290.25760.3595RANDOM69.311
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]
-3.55-4.417.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.194
r_dihedral_angle_3_deg17.987
r_dihedral_angle_4_deg16.284
r_dihedral_angle_1_deg8.533
r_angle_refined_deg1.554
r_angle_other_deg1.088
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.194
r_dihedral_angle_3_deg17.987
r_dihedral_angle_4_deg16.284
r_dihedral_angle_1_deg8.533
r_angle_refined_deg1.554
r_angle_other_deg1.088
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2862
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing