3CC9

Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O1OPDB entry 2O1O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529319% PEG 3350, 0.2 M MgCl2, 1mM GGPP, 2mM MgCl2, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.095α = 90
b = 108.985β = 90
c = 141.354γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.3501000.0620.03511.77.2739837398356
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)
2.32.381000.6351.677327

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 2O1O2.334.617384773847372099.670.2430.2430.2410.296RANDOM57.439
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]
0.060.03-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.853
r_dihedral_angle_4_deg17.94
r_dihedral_angle_3_deg15.341
r_dihedral_angle_1_deg4.388
r_scangle_it1.192
r_angle_refined_deg1.08
r_scbond_it0.749
r_mcangle_it0.575
r_mcbond_it0.305
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.853
r_dihedral_angle_4_deg17.94
r_dihedral_angle_3_deg15.341
r_dihedral_angle_1_deg4.388
r_scangle_it1.192
r_angle_refined_deg1.08
r_scbond_it0.749
r_mcangle_it0.575
r_mcbond_it0.305
r_nbtor_refined0.295
r_nbd_refined0.184
r_symmetry_vdw_refined0.177
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.086
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10866
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms115

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction