2A0S

Crystal structure of 6-pyruvoyl tetrahydropterin synthase (PTPS) from Plasmodium vivax at 2.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y13pdb entry 1Y13

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629818% w/v PEG4000, 0.05 M Sodium Acetate pH 4.6 , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.160.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.095α = 90
b = 132.095β = 90
c = 74.126γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.0ALS8.2.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.25091.780.0611.93.52132133.75
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.31962.610.42.32.42120

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTpdb entry 1Y132.25021321115291.780.210230.210230.208380.24575RANDOM35.155
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]
-0.26-0.13-0.260.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_3_deg12.398
r_dihedral_angle_4_deg7.868
r_dihedral_angle_1_deg5.196
r_scangle_it1.835
r_mcangle_it1.342
r_scbond_it1.101
r_angle_refined_deg0.905
r_mcbond_it0.78
r_nbtor_refined0.292
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.935
r_dihedral_angle_3_deg12.398
r_dihedral_angle_4_deg7.868
r_dihedral_angle_1_deg5.196
r_scangle_it1.835
r_mcangle_it1.342
r_scbond_it1.101
r_angle_refined_deg0.905
r_mcbond_it0.78
r_nbtor_refined0.292
r_nbd_refined0.161
r_symmetry_vdw_refined0.129
r_xyhbond_nbd_refined0.089
r_symmetry_hbond_refined0.088
r_chiral_restr0.057
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2652
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing