5HN8

Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5291200MM LISO4, 20% PEG3350, 100MM TRIS, PH 8.5, HANGING DROP, TEMPERATURE 291K
Crystal Properties
Matthews coefficientSolvent content
2.2244.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.072α = 90
b = 117.22β = 116.2
c = 92.786γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDMARMOSAIC 225 mm CCD2010-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.9787APS21-ID-F

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
12.75099.50.1269.25.3439201
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)
12.72.7597.50.5613.9

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 REPLACEMENTTHROUGHOUT3LDW2.731.1386622075920.2610.2590.296RANDOM47.09
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]
0.08-0.210.21-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.845
r_dihedral_angle_3_deg17.512
r_dihedral_angle_4_deg16.561
r_dihedral_angle_1_deg5.706
r_scangle_it5.307
r_scbond_it3.005
r_mcangle_it1.95
r_angle_refined_deg1.407
r_mcbond_it0.928
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.845
r_dihedral_angle_3_deg17.512
r_dihedral_angle_4_deg16.561
r_dihedral_angle_1_deg5.706
r_scangle_it5.307
r_scbond_it3.005
r_mcangle_it1.95
r_angle_refined_deg1.407
r_mcbond_it0.928
r_chiral_restr0.105
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
MAIN-CHAIN ANGLE OTHER ATOMS (A**2)
SIDE-CHAIN BOND OTHER ATOMS (A**2)
SIDE-CHAIN ANGLE OTHER ATOMS (A**2)
LONG RANGE B REFINED ATOMS (A**2)
LONG RANGE B OTHER ATOMS (A**2)
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10497
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing