2Q8L

Crystal structure of orotidine 5'-phosphate decarboxylase from Plasmodium falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F84PDB entry 2F84

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529315% PEG 10000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.563α = 90
b = 70.909β = 90
c = 70.201γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.978565APS19-ID

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
12.124.9597.150.0650.06511.89.31942319423
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)
12.12.141000.2670.2677.399.61015

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 2F842.124.95194231942359797.150.217460.217460.216430.24929RANDOM35.622
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]
-1.77-0.111.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.853
r_dihedral_angle_4_deg23.714
r_dihedral_angle_3_deg18.192
r_dihedral_angle_1_deg7.315
r_scangle_it3.467
r_scbond_it2.729
r_mcangle_it1.618
r_angle_refined_deg1.464
r_mcbond_it1.258
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.853
r_dihedral_angle_4_deg23.714
r_dihedral_angle_3_deg18.192
r_dihedral_angle_1_deg7.315
r_scangle_it3.467
r_scbond_it2.729
r_mcangle_it1.618
r_angle_refined_deg1.464
r_mcbond_it1.258
r_nbtor_refined0.312
r_symmetry_hbond_refined0.233
r_nbd_refined0.212
r_symmetry_vdw_refined0.212
r_xyhbond_nbd_refined0.168
r_chiral_restr0.117
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms5

Software

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