3N2M

Crystal structure of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q8L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.6293PEG 1000, ammonium phosphate, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8934.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.64α = 90
b = 83.35β = 90
c = 89.843γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.90020APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.85099.90.0760.07610.67.85664954815
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831000.4660.4664.337.92803

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 REPLACEMENTTHROUGHOUT2Q8L1.85053736287299.690.156720.154930.18895RANDOM17.789
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]
-0.010.35-0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.588
r_dihedral_angle_4_deg22.276
r_dihedral_angle_3_deg13.555
r_dihedral_angle_1_deg6.223
r_scangle_it4.455
r_scbond_it2.716
r_mcangle_it1.635
r_angle_refined_deg1.554
r_mcbond_it0.906
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.588
r_dihedral_angle_4_deg22.276
r_dihedral_angle_3_deg13.555
r_dihedral_angle_1_deg6.223
r_scangle_it4.455
r_scbond_it2.716
r_mcangle_it1.635
r_angle_refined_deg1.554
r_mcbond_it0.906
r_chiral_restr0.115
r_bond_refined_d0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5345
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms70

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling