3BPW

Crystal Structure of P. falciparum Orotidine 5'-monophosphate Decarboxylase Complexed with XMP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.229330% PEG 1000, 100mM Ammonium Phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.20
Crystal Properties
Matthews coefficientSolvent content
1.935.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.902α = 90
b = 83.582β = 90
c = 89.793γ = 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 SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR2007-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-1CLSI08ID-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
11.75099.50.0680.06811.24.666788
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)
11.71.7695.60.3940.3942.63.5

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 REPLACEMENTTHROUGHOUT2Q8L1.7506410263705339499.40.1720.170.205RANDOM18.72
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]
-0.010.22-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.05
r_dihedral_angle_4_deg20.515
r_dihedral_angle_3_deg13.739
r_dihedral_angle_1_deg6.124
r_scangle_it3.94
r_scbond_it2.731
r_mcangle_it1.668
r_angle_refined_deg1.553
r_mcbond_it1.079
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.05
r_dihedral_angle_4_deg20.515
r_dihedral_angle_3_deg13.739
r_dihedral_angle_1_deg6.124
r_scangle_it3.94
r_scbond_it2.731
r_mcangle_it1.668
r_angle_refined_deg1.553
r_mcbond_it1.079
r_nbtor_refined0.318
r_symmetry_vdw_refined0.241
r_nbd_refined0.214
r_symmetry_hbond_refined0.158
r_xyhbond_nbd_refined0.127
r_chiral_restr0.112
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5352
Nucleic Acid Atoms
Solvent Atoms366
Heterogen Atoms60

Software

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