2FDS

Crystal Structure of Plasmodium Berghei Orotidine 5'-monophosphate Decarboxylase (ortholog of Plasmodium falciparum PF10_0225)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AQWPDB Entry: 2AQW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29116% Peg3350, 140mM diammonium hydrogen citrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0339.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.202α = 90
b = 108.623β = 97.3
c = 69.89γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-10-31SINGLE WAVELENGTH
21x-ray
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
1,21.725094.40.047365456
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)
1.721.78670.3821.94637

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB Entry: 2AQW1.7229.2265422330894.270.1880.1860.221RANDOM25.168
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.674
r_dihedral_angle_4_deg17.932
r_dihedral_angle_3_deg13.629
r_dihedral_angle_1_deg5.715
r_mcangle_it2.034
r_scangle_it2.028
r_scbond_it1.374
r_angle_refined_deg1.314
r_mcbond_it1.276
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.674
r_dihedral_angle_4_deg17.932
r_dihedral_angle_3_deg13.629
r_dihedral_angle_1_deg5.715
r_mcangle_it2.034
r_scangle_it2.028
r_scbond_it1.374
r_angle_refined_deg1.314
r_mcbond_it1.276
r_nbtor_refined0.306
r_nbd_refined0.214
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.135
r_chiral_restr0.105
r_symmetry_hbond_refined0.092
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5438
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms2

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction