3F0D

High resolution crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphatase synthase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289PACT screen condition c8, 0.1 M Tris HCL, 20% PEG 4000, 0.2 M NaCl, 34.4. mg/mL protein, 0.4 uL/0.4 uL drops, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0840.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 157.887α = 90
b = 69.042β = 130.15
c = 116.581γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002008-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

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
11.25093.30.08115.84271861
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)
11.21.290.522.23.324496

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.2502718611374591.160.1860.1850.209RANDOM20.638
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]
-1.75-0.971.94-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.309
r_dihedral_angle_3_deg14.946
r_dihedral_angle_4_deg13.608
r_sphericity_free10.168
r_sphericity_bonded6.366
r_dihedral_angle_1_deg5.739
r_scangle_it4.946
r_scbond_it3.459
r_mcangle_it2.628
r_mcbond_it1.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.309
r_dihedral_angle_3_deg14.946
r_dihedral_angle_4_deg13.608
r_sphericity_free10.168
r_sphericity_bonded6.366
r_dihedral_angle_1_deg5.739
r_scangle_it4.946
r_scbond_it3.459
r_mcangle_it2.628
r_mcbond_it1.776
r_rigid_bond_restr1.692
r_angle_refined_deg1.663
r_angle_other_deg1.019
r_mcbond_other0.991
r_chiral_restr0.11
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6705
Nucleic Acid Atoms
Solvent Atoms504
Heterogen Atoms6

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling