2Q8Z

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q8LPDB entry 2Q8L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729330% PEG 1000, 100mM Ammonium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9637.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.497α = 90
b = 83.885β = 90
c = 89.608γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-23MSINGLE 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
11.85094.410.0970.09710.14.95132851328
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)
11.81.83970.4350.4352.74.82826

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 2Q8L1.824.575132851328275294.410.169160.169160.166930.21171RANDOM22.266
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]
-0.060.8-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.903
r_dihedral_angle_4_deg22.086
r_dihedral_angle_3_deg14.657
r_dihedral_angle_1_deg6.269
r_scangle_it4.058
r_scbond_it2.736
r_mcangle_it1.673
r_angle_refined_deg1.502
r_mcbond_it1.085
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.903
r_dihedral_angle_4_deg22.086
r_dihedral_angle_3_deg14.657
r_dihedral_angle_1_deg6.269
r_scangle_it4.058
r_scbond_it2.736
r_mcangle_it1.673
r_angle_refined_deg1.502
r_mcbond_it1.085
r_nbtor_refined0.317
r_symmetry_hbond_refined0.292
r_symmetry_vdw_refined0.242
r_nbd_refined0.209
r_xyhbond_nbd_refined0.129
r_chiral_restr0.11
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5354
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms72

Software

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