3LZE

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS), E37C catalytic residue mutant


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LX33lx3 with mutation and without ligand

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22982 ul 17 mg/ml protein (in SGPP buffer) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 1 mM TCEP; 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
2.9257.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.495α = 90
b = 131.495β = 90
c = 73.67γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-06-18MSINGLE 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
11.93099.90.07714.59.219289543
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)
1.91.971000.6612.59.41896

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 with mutation and without ligand1.929.0319289100599.850.1930.1910.22RANDOM49.531
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]
-1.81-0.9-1.812.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.703
r_dihedral_angle_4_deg22.421
r_dihedral_angle_3_deg14.5
r_scangle_it6.613
r_dihedral_angle_1_deg6.417
r_scbond_it4.7
r_mcangle_it4.025
r_mcbond_it2.775
r_angle_refined_deg1.542
r_mcbond_other0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.703
r_dihedral_angle_4_deg22.421
r_dihedral_angle_3_deg14.5
r_scangle_it6.613
r_dihedral_angle_1_deg6.417
r_scbond_it4.7
r_mcangle_it4.025
r_mcbond_it2.775
r_angle_refined_deg1.542
r_mcbond_other0.96
r_angle_other_deg0.862
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1374
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms13

Software

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