3LX3

Plasmodium vivax 6-pyruvoyltetrahydropterin synthase (PTPS) in complex with xanthopterin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A0S2a0s, A chain

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22982 ul 5 mg/ml protein (refolded in SGPP buffer + 0.01 mM Zn2+) mixed with 1 ul 0.1 M sodium acetate (pH 5.2), 24% PEG 3350, 10 mM MgCl2, 1 mM TCEP, 2 mM xanthopterin; cryoprotected by 3 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
2.9157.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 131.358α = 90
b = 131.358β = 90
c = 73.577γ = 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
11.555099.60.05712.8935343428
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)
1.551.6196.30.7621.86.53414

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 REPLACEMENTTHROUGHOUT2a0s, A chain1.5537.1235342183599.550.150.1490.167RANDOM25.948
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]
-0.95-0.47-0.951.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.795
r_dihedral_angle_4_deg20.364
r_dihedral_angle_3_deg12.139
r_dihedral_angle_1_deg6.475
r_scangle_it6.269
r_scbond_it3.97
r_mcangle_it2.871
r_mcbond_it1.783
r_angle_refined_deg1.676
r_angle_other_deg0.939
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.795
r_dihedral_angle_4_deg20.364
r_dihedral_angle_3_deg12.139
r_dihedral_angle_1_deg6.475
r_scangle_it6.269
r_scbond_it3.97
r_mcangle_it2.871
r_mcbond_it1.783
r_angle_refined_deg1.676
r_angle_other_deg0.939
r_mcbond_other0.605
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1396
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms14

Software

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