3M0N

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37A catalytic residue mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LX33lx3, ligand removed and with E37 mutated to A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22982 ul 25 mg/ml protein (in SGPP buffer) mixed with 2 ul 0.1 M sodium acetate (pH 5.2), 28% PEG 3350, 5 mM DTT; cryoprotected by 5 sec dip in 96 mM sodium acetate (pH 5.2), 24% PEG 3350, 134 mM NaCl, 20% glycerol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9658.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.75α = 90
b = 131.75β = 90
c = 74.24γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.95099.80.07912.99.319474543
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.971000.6832.49.41947

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3lx3, ligand removed and with E37 mutated to A1.935.319465101199.680.1980.1960.225RANDOM49.913
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]
-2.45-1.22-2.453.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.27
r_dihedral_angle_4_deg22.495
r_dihedral_angle_3_deg13.13
r_dihedral_angle_1_deg6.283
r_scangle_it5.07
r_scbond_it3.354
r_mcangle_it2.892
r_mcbond_it1.976
r_angle_refined_deg1.243
r_angle_other_deg0.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.27
r_dihedral_angle_4_deg22.495
r_dihedral_angle_3_deg13.13
r_dihedral_angle_1_deg6.283
r_scangle_it5.07
r_scbond_it3.354
r_mcangle_it2.892
r_mcbond_it1.976
r_angle_refined_deg1.243
r_angle_other_deg0.806
r_mcbond_other0.642
r_chiral_restr0.076
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1364
Nucleic Acid Atoms
Solvent Atoms62
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing