3BAR

Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-azido-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 DROP9.2293100mM Ammonium phosphate, 27% PEG 1000, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.935.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.928α = 90
b = 83.354β = 90
c = 89.872γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDDCM with cryo-cooled 1st crystal sagitally bent 2nd crystal followed by vertically focusing mirror2007-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97934CLSI08ID-1

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
11.95095.370.0850.08511.45.24415544155
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)
11.91.9797.90.4590.4593.455.14703

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 2Q8L1.924.684415544155235795.370.174450.174450.172020.2193RANDOM22.075
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]
0.49-0.19-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.745
r_dihedral_angle_4_deg24.013
r_dihedral_angle_3_deg14.035
r_dihedral_angle_1_deg5.871
r_scangle_it3.725
r_scbond_it2.53
r_mcangle_it1.613
r_angle_refined_deg1.518
r_mcbond_it1.017
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.745
r_dihedral_angle_4_deg24.013
r_dihedral_angle_3_deg14.035
r_dihedral_angle_1_deg5.871
r_scangle_it3.725
r_scbond_it2.53
r_mcangle_it1.613
r_angle_refined_deg1.518
r_mcbond_it1.017
r_nbtor_refined0.316
r_nbd_refined0.228
r_symmetry_vdw_refined0.222
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.146
r_chiral_restr0.107
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5308
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms42

Software

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