2VWT

Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DXEPDB ENTRY 1DXE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE HOMOLOGUE FROM ESCHERICHIA COLI K12. ACTA CRYST. D58, 2191-2193., pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.547

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.6α = 90
b = 137.7β = 90
c = 124.1γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2005-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

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
11.9353940.0432.24.663843-331.4
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)
11.93295.50.342.73.3

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 DIFFRACTIONMADTHROUGHOUTPDB ENTRY 1DXE1.9352.7612642579940.1690.1680.206RANDOM37.47
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]
2.66-0.98-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.012
r_dihedral_angle_3_deg14.055
r_dihedral_angle_4_deg11.714
r_dihedral_angle_1_deg6.82
r_scangle_it3.183
r_scbond_it2.163
r_angle_refined_deg1.475
r_mcangle_it1.416
r_mcbond_it0.912
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.012
r_dihedral_angle_3_deg14.055
r_dihedral_angle_4_deg11.714
r_dihedral_angle_1_deg6.82
r_scangle_it3.183
r_scbond_it2.163
r_angle_refined_deg1.475
r_mcangle_it1.416
r_mcbond_it0.912
r_nbtor_refined0.304
r_nbd_refined0.2
r_symmetry_vdw_refined0.165
r_symmetry_hbond_refined0.128
r_xyhbond_nbd_refined0.124
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.006
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_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5853
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing