2QAF

Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-iodo-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 DROP7.429330% PEG 1000, 100mM Ammonium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9135.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.92α = 90
b = 83.849β = 90
c = 89.869γ = 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
11.955095.430.1020.1029.14.74330341322
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)
11.951.98980.4920.4922.34.32199

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2Q8L1.9528.34302741065219195.440.174530.171830.2258RANDOM19.806
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]
0.550.28-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.403
r_dihedral_angle_4_deg24.152
r_dihedral_angle_3_deg14.8
r_dihedral_angle_1_deg6.198
r_scangle_it4.188
r_scbond_it2.885
r_mcangle_it1.73
r_angle_refined_deg1.633
r_mcbond_it1.152
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.403
r_dihedral_angle_4_deg24.152
r_dihedral_angle_3_deg14.8
r_dihedral_angle_1_deg6.198
r_scangle_it4.188
r_scbond_it2.885
r_mcangle_it1.73
r_angle_refined_deg1.633
r_mcbond_it1.152
r_nbtor_refined0.315
r_nbd_refined0.232
r_symmetry_hbond_refined0.213
r_symmetry_vdw_refined0.188
r_xyhbond_nbd_refined0.158
r_chiral_restr0.12
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 Atoms250
Heterogen Atoms47

Software

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