5J04

Crystal structure of Enolase from Synechococcus elongatus, complex with phosphoenolpyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E9I 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529810-15% PEG200, 150-200mM CaAcetate, 0.1M Hepes pH 7.5, 10mM PEP
Crystal Properties
Matthews coefficientSolvent content
2.7355.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.23α = 90
b = 164.23β = 90
c = 72.68γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.282.1198.40.20.2420.080.9826.78.850150
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)
12.22.2784.60.366.1

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 REPLACEMENTTHROUGHOUT1e9i2.373.5542379218999.70.214490.212880.24494RANDOM30.054
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]
-2.04-2.044.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.362
r_dihedral_angle_4_deg18.876
r_dihedral_angle_3_deg15.014
r_dihedral_angle_1_deg6.823
r_long_range_B_refined5.551
r_long_range_B_other5.543
r_scangle_other4.345
r_mcangle_it3.489
r_mcangle_other3.488
r_scbond_it2.761
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.362
r_dihedral_angle_4_deg18.876
r_dihedral_angle_3_deg15.014
r_dihedral_angle_1_deg6.823
r_long_range_B_refined5.551
r_long_range_B_other5.543
r_scangle_other4.345
r_mcangle_it3.489
r_mcangle_other3.488
r_scbond_it2.761
r_scbond_other2.76
r_mcbond_it2.339
r_mcbond_other2.332
r_angle_refined_deg1.574
r_angle_other_deg1.327
r_chiral_restr0.073
r_bond_refined_d0.009
r_gen_planes_refined0.007
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6278
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
PHASERphasing