3MBM

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine and 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 3IKEPDB entry 3ike

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP828920% PEG 4000, 100 mM Tris, 200 mM NaCl, 5 mM ZnCl2 with 34.4 mg/mL protein for 3 days. Crystal soaked in 25 mM cytosine and fragment 717 in same buffer for 3 weeks. VAPOR DIFFUSION, SITTING DROP, temperature 289K, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.0339.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.543α = 90
b = 67.569β = 96.12
c = 60.03γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-02-22MSINGLE 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
11.85088.40.08120.11.741626
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)
11.81.8381.60.2562.521.23545

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 3ike1.825.541626209095.950.1890.1880.217RANDOM6.423
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.355
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg13.26
r_dihedral_angle_1_deg5.635
r_scangle_it2.608
r_angle_refined_deg1.745
r_scbond_it1.703
r_angle_other_deg1.078
r_mcangle_it1.028
r_mcbond_it0.591
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.355
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg13.26
r_dihedral_angle_1_deg5.635
r_scangle_it2.608
r_angle_refined_deg1.745
r_scbond_it1.703
r_angle_other_deg1.078
r_mcangle_it1.028
r_mcbond_it0.591
r_mcbond_other0.136
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3417
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms65

Software

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