3IEQ

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F0Epdb entry 3F0E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9289JCSG+ condition A5, 20% PEG 3350, 0.2 M Magnesium formate, 34.4 mg/mL protein, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0439.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.27α = 90
b = 67.7β = 96.38
c = 60.34γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-07-01MSINGLE 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
12.119.4291.50.03720.986088325206-328.685
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)
12.12.1587.80.1585.91783

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 3F0E2.119.4225204124991.650.1750.1720.225RANDOM22.275
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]
-0.150.030.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.553
r_dihedral_angle_4_deg15.425
r_dihedral_angle_3_deg14.057
r_dihedral_angle_1_deg4.896
r_scangle_it2.497
r_scbond_it1.525
r_angle_refined_deg1.086
r_mcangle_it1.064
r_mcbond_it0.58
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.553
r_dihedral_angle_4_deg15.425
r_dihedral_angle_3_deg14.057
r_dihedral_angle_1_deg4.896
r_scangle_it2.497
r_scbond_it1.525
r_angle_refined_deg1.086
r_mcangle_it1.064
r_mcbond_it0.58
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3427
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms56

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction