3B6N

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.529325% PEG 3350, 0.1 M Citric acid pH 3.5, 2 mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0840.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.661α = 90
b = 79.661β = 90
c = 79.661γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

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
12.26501000.1050.078.918.38156815653.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.262.3499.90.89580.71771.576.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1VH82.2639.848159815637699.960.206640.204050.25746RANDOM45.102
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.39
r_dihedral_angle_3_deg19.282
r_dihedral_angle_4_deg12.583
r_dihedral_angle_1_deg8.023
r_scangle_it4.695
r_scbond_it3.047
r_mcangle_it1.94
r_angle_refined_deg1.835
r_mcbond_it1.121
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.39
r_dihedral_angle_3_deg19.282
r_dihedral_angle_4_deg12.583
r_dihedral_angle_1_deg8.023
r_scangle_it4.695
r_scbond_it3.047
r_mcangle_it1.94
r_angle_refined_deg1.835
r_mcbond_it1.121
r_nbtor_refined0.308
r_symmetry_hbond_refined0.22
r_nbd_refined0.217
r_symmetry_vdw_refined0.207
r_xyhbond_nbd_refined0.162
r_chiral_restr0.123
r_bond_refined_d0.021
r_gen_planes_refined0.007
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 Atoms1138
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms1

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction