3IKE

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei with cytosine


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, 0.4/0.4 uL drops, Crystal tracking ID 204112a1, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2846.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.659α = 90
b = 68.064β = 96.29
c = 60.156γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-07-28MSINGLE 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
12.35099.90.08912.83.221121
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)
12.32.381000.412.83.22105

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 3F0E2.328.3121111108499.70.1870.1850.234RANDOM26.741
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]
-1.360.141.62-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.953
r_dihedral_angle_4_deg18.757
r_dihedral_angle_3_deg15.073
r_dihedral_angle_1_deg5.78
r_scangle_it3.438
r_scbond_it2.161
r_mcangle_it1.473
r_angle_refined_deg1.442
r_mcbond_it0.816
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.953
r_dihedral_angle_4_deg18.757
r_dihedral_angle_3_deg15.073
r_dihedral_angle_1_deg5.78
r_scangle_it3.438
r_scbond_it2.161
r_mcangle_it1.473
r_angle_refined_deg1.442
r_mcbond_it0.816
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3398
Nucleic Acid Atoms
Solvent Atoms241
Heterogen Atoms29

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling