3N3M

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.8293PEG 1000, ammonium phosphate, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.8935.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.802α = 90
b = 83.131β = 90
c = 89.983γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE A10.97710CHESSA1

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
11.475099.50.0610.06110.97.210317299916
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)
11.471.591.80.4970.4972.885.54685

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2Q8L1.475097966515199.50.164140.162720.19105RANDOM17.292
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]
0.09-0.160.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.787
r_dihedral_angle_4_deg22.868
r_dihedral_angle_3_deg13.286
r_dihedral_angle_1_deg6.091
r_scangle_it3.739
r_scbond_it2.542
r_mcangle_it1.577
r_angle_refined_deg1.54
r_mcbond_it0.992
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.787
r_dihedral_angle_4_deg22.868
r_dihedral_angle_3_deg13.286
r_dihedral_angle_1_deg6.091
r_scangle_it3.739
r_scbond_it2.542
r_mcangle_it1.577
r_angle_refined_deg1.54
r_mcbond_it0.992
r_nbtor_refined0.319
r_nbd_refined0.222
r_symmetry_vdw_refined0.222
r_symmetry_hbond_refined0.187
r_xyhbond_nbd_refined0.132
r_chiral_restr0.108
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5345
Nucleic Acid Atoms
Solvent Atoms597
Heterogen Atoms91

Software

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