5GY7

X-Ray structure of H243I mutant of UDP-Galactose 4-epimerase from E.coli:evidence for existence of open and closed active site during catalysis.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72770.2M Ammonium Nitrate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.0840.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.11α = 90
b = 91.16β = 99.87
c = 80.26γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2016-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.00ELETTRA5.2R

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
11.4379.0798.77.733.3121857

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 REPLACEMENTTHROUGHOUT1XEL1.4379.07115821603698.670.135170.133880.16014RANDOM10.625
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]
0.53-0.08-0.06-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.032
r_dihedral_angle_4_deg12.929
r_dihedral_angle_3_deg10.921
r_dihedral_angle_1_deg6.034
r_long_range_B_refined4.278
r_long_range_B_other4.032
r_scangle_other2.932
r_angle_refined_deg2.454
r_scbond_it2.093
r_scbond_other2.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.032
r_dihedral_angle_4_deg12.929
r_dihedral_angle_3_deg10.921
r_dihedral_angle_1_deg6.034
r_long_range_B_refined4.278
r_long_range_B_other4.032
r_scangle_other2.932
r_angle_refined_deg2.454
r_scbond_it2.093
r_scbond_other2.089
r_mcangle_other1.762
r_mcangle_it1.758
r_mcbond_it1.204
r_mcbond_other1.181
r_angle_other_deg1.157
r_chiral_restr0.148
r_bond_refined_d0.027
r_gen_planes_refined0.013
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms5142
Nucleic Acid Atoms
Solvent Atoms644
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing