4ONV

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Microbatch under oil6.529815%PEG 3350, 100mM Hepes pH 6.5, 200mM MgCl2, Microbatch under oil, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.17α = 90
b = 155.41β = 90
c = 55.51γ = 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 BM140.974ESRFBM14

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
11.9919.7998.60.4054.8183685-3
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)
11.992.0491.20.0350.44

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 REPLACEMENTTHROUGHOUT2.5719.7937422197098.910.248480.246580.2845RANDOM22.637
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]
-2.834.22-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.236
r_dihedral_angle_4_deg22.325
r_dihedral_angle_3_deg15.102
r_dihedral_angle_1_deg6.004
r_mcangle_it1.965
r_angle_refined_deg1.476
r_scbond_it1.316
r_mcbond_it1.229
r_mcbond_other1.228
r_angle_other_deg1.186
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.236
r_dihedral_angle_4_deg22.325
r_dihedral_angle_3_deg15.102
r_dihedral_angle_1_deg6.004
r_mcangle_it1.965
r_angle_refined_deg1.476
r_scbond_it1.316
r_mcbond_it1.229
r_mcbond_other1.228
r_angle_other_deg1.186
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms9037
Nucleic Acid Atoms
Solvent Atoms200
Heterogen Atoms182

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction