3IEW

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with bound CTP and CDP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9293JCSG+ screen condition A5, 20% PEG 3350, 0.2 M Magnesium formate, 34.4 mg/mL Protein, 0.4/0.4 microliter drops, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0339.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.703α = 90
b = 67.548β = 95.85
c = 60.152γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944Mirrors2009-06-29MSINGLE 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
12.15099.70.069.33.727409
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)
12.12.1495.30.3493.1

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 3F0E2.1502739913820.2020.1990.248RANDOM26.94
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]
-1.411.450.980.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.082
r_dihedral_angle_3_deg14.464
r_dihedral_angle_4_deg12.472
r_dihedral_angle_1_deg5.351
r_scangle_it2.64
r_scbond_it1.623
r_mcangle_it1.292
r_angle_refined_deg1.272
r_angle_other_deg0.844
r_mcbond_it0.707
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.082
r_dihedral_angle_3_deg14.464
r_dihedral_angle_4_deg12.472
r_dihedral_angle_1_deg5.351
r_scangle_it2.64
r_scbond_it1.623
r_mcangle_it1.292
r_angle_refined_deg1.272
r_angle_other_deg0.844
r_mcbond_it0.707
r_mcbond_other0.124
r_chiral_restr0.07
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3413
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms88

Software

Software
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling