3EZ3

Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529320 % PEG3350 0.2 M Li2SO4 0.1 M Tris 8.5 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.346.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.266α = 90
b = 109.696β = 90
c = 139.529γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702007-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCHESS BEAMLINE F10.9197CHESSF1

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
12.304251000.1840.12710.6677.3725857251544.9
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)
12.3042.4999.90.6891.477173

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.30424.437594072250363395.130.2290.2290.2260.291RANDOM24.385
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]
-0.010.1-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.799
r_dihedral_angle_4_deg20.629
r_dihedral_angle_3_deg17.325
r_dihedral_angle_1_deg6.116
r_scangle_it2.648
r_scbond_it1.819
r_angle_refined_deg1.649
r_mcangle_it1.105
r_mcbond_it0.661
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.799
r_dihedral_angle_4_deg20.629
r_dihedral_angle_3_deg17.325
r_dihedral_angle_1_deg6.116
r_scangle_it2.648
r_scbond_it1.819
r_angle_refined_deg1.649
r_mcangle_it1.105
r_mcbond_it0.661
r_nbtor_refined0.307
r_symmetry_vdw_refined0.264
r_nbd_refined0.215
r_xyhbond_nbd_refined0.181
r_chiral_restr0.115
r_symmetry_hbond_refined0.098
r_metal_ion_refined0.075
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11546
Nucleic Acid Atoms
Solvent Atoms561
Heterogen Atoms158

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection