2POD

Crystal structure of a member of enolase superfamily from Burkholderia pseudomallei K96243


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5294100mM Bis-Tris-HCl, pH 5.5, 45% MPD, 200mM Ammonium acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4553

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 146.771α = 90
b = 146.771β = 90
c = 85.531γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2006-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97960APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.345088.80.090.0715.23.73837938379-547
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.4286.20.60.420.92.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.34203365633656107690.730.21140.21140.209370.27451RANDOM51.783
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]
-1.6-1.63.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.527
r_dihedral_angle_3_deg21.516
r_dihedral_angle_4_deg15.577
r_scangle_it8.904
r_dihedral_angle_1_deg8.807
r_scbond_it6.558
r_mcangle_it4.182
r_mcbond_it2.585
r_angle_refined_deg1.272
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.527
r_dihedral_angle_3_deg21.516
r_dihedral_angle_4_deg15.577
r_scangle_it8.904
r_dihedral_angle_1_deg8.807
r_scbond_it6.558
r_mcangle_it4.182
r_mcbond_it2.585
r_angle_refined_deg1.272
r_nbtor_refined0.296
r_xyhbond_nbd_refined0.162
r_nbd_refined0.143
r_symmetry_hbond_refined0.14
r_chiral_restr0.121
r_symmetry_vdw_refined0.102
r_metal_ion_refined0.031
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5967
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms2

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing