4OE7

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V8Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH UNDER OIL6.5298100mM HEPES pH 6.5, 200mM Magnesium chloride, 15% PEG 3350, MICROBATCH UNDER OIL, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.24α = 90
b = 155.14β = 90
c = 55.58γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2012-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97625ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.998.8998.214.434.183414
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.992.04872.763.42

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2V8Z1.9949.068341479242417198.270.19980.198040.23308RANDOM19.011
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]
-1.331.10.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.378
r_dihedral_angle_4_deg21.045
r_dihedral_angle_3_deg12.478
r_dihedral_angle_1_deg6.229
r_long_range_B_other4.106
r_long_range_B_refined4.105
r_scangle_other3.191
r_scbond_other2.19
r_scbond_it2.161
r_mcangle_it1.946
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.378
r_dihedral_angle_4_deg21.045
r_dihedral_angle_3_deg12.478
r_dihedral_angle_1_deg6.229
r_long_range_B_other4.106
r_long_range_B_refined4.105
r_scangle_other3.191
r_scbond_other2.19
r_scbond_it2.161
r_mcangle_it1.946
r_mcangle_other1.943
r_angle_refined_deg1.896
r_mcbond_it1.436
r_mcbond_other1.435
r_angle_other_deg1.356
r_chiral_restr0.127
r_bond_refined_d0.021
r_bond_other_d0.01
r_gen_planes_refined0.009
r_gen_planes_other0.003
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 Atoms9037
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms192

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling