3P10

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytidine and FOL694, 2-(thiophen-2-yl)phenyl methanol


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP828927 mg/mL protein in 20% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2. Crystals soaked in 25 mM cytidine and FOL694 in same buffer for 3 weeks, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0339.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.54α = 90
b = 67.55β = 95.99
c = 60.07γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-08-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

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
11.72098.40.02230.4250700-3
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)
11.71.7488.30.1175.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.719.9148085257098.420.160490.158830.19183RANDOM21.331
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_deg31.856
r_dihedral_angle_4_deg17.823
r_dihedral_angle_3_deg13.137
r_dihedral_angle_1_deg5.347
r_scangle_it3.166
r_scbond_it1.994
r_angle_refined_deg1.427
r_mcangle_it1.401
r_mcbond_it0.819
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.856
r_dihedral_angle_4_deg17.823
r_dihedral_angle_3_deg13.137
r_dihedral_angle_1_deg5.347
r_scangle_it3.166
r_scbond_it1.994
r_angle_refined_deg1.427
r_mcangle_it1.401
r_mcbond_it0.819
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.006
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3473
Nucleic Acid Atoms
Solvent Atoms398
Heterogen Atoms69

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction