2F84

Crystal Structure of an orotidine-5'-monophosphate decarboxylase homolog from P.falciparum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AQW2AQW.pdb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.2298100mM Ammonium Phosphate, 18% PEG 1000, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2545.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.911α = 90
b = 69.057β = 90
c = 69.735γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
1269.7496.10.1020.1024.93.82269811
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)
122.1185.80.7850.7850.73.22896

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 REPLACEMENTTHROUGHOUT2AQW.pdb2.118.61226981976698796.040.230.230.2270.288RANDOM11.496
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]
-0.59-0.280.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.745
r_dihedral_angle_4_deg19.772
r_dihedral_angle_3_deg15.685
r_dihedral_angle_1_deg6.33
r_scangle_it2.815
r_scbond_it2.052
r_angle_refined_deg1.475
r_mcangle_it1.412
r_mcbond_it0.886
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.745
r_dihedral_angle_4_deg19.772
r_dihedral_angle_3_deg15.685
r_dihedral_angle_1_deg6.33
r_scangle_it2.815
r_scbond_it2.052
r_angle_refined_deg1.475
r_mcangle_it1.412
r_mcbond_it0.886
r_nbtor_refined0.309
r_symmetry_vdw_refined0.216
r_nbd_refined0.212
r_symmetry_hbond_refined0.202
r_xyhbond_nbd_refined0.168
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2662
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms5

Software

Software
Software NamePurpose
SCALAdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling