3IKF

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with FOL fragment 717, imidazo[2,,1-b][1,3]thiazol-6-ylmethanol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F0EPDB entry 3F0E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.928920% PEG 3350, 0.2 M Mg formate, 34.4 mg/mL protein, 20 mM FOL 717, 10 mM ZnCl2, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2545.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.01α = 90
b = 67.65β = 96.27
c = 60.09γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-07-31MSINGLE 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)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
12.072094.40.03330.2926980-328.092
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)
12.072.1282.80.1418.71735

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 REPLACEMENTTHROUGHOUTPDB entry 3F0E2.0719.4926979137494.580.1780.1750.221RANDOM23.615
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]
-0.11-0.010.15-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.396
r_dihedral_angle_4_deg18.422
r_dihedral_angle_3_deg14.069
r_dihedral_angle_1_deg5.148
r_scangle_it2.983
r_scbond_it1.867
r_angle_refined_deg1.656
r_mcangle_it1.35
r_mcbond_it0.75
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.396
r_dihedral_angle_4_deg18.422
r_dihedral_angle_3_deg14.069
r_dihedral_angle_1_deg5.148
r_scangle_it2.983
r_scbond_it1.867
r_angle_refined_deg1.656
r_mcangle_it1.35
r_mcbond_it0.75
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3410
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms39

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction