5U24

X-ray structure of the WlaRG aminotransferase from campylobacter jejuni, K184A mutant in complex with TDP-Fuc3N


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5U1Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MOPS (pH7) 13-17% PEG-5000 10 mM TDP-Fuc3N 1 mM PLP
Crystal Properties
Matthews coefficientSolvent content
2.1943.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.057α = 90
b = 56.795β = 90.02
c = 124.306γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-09-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.75096.60.0510.05137.33.9160895
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)
11.71.7689.40.16562.514759

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 REPLACEMENTTHROUGHOUT5u1z1.728.53152750834896.330.10710.105020.14627RANDOM19.926
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]
16.52-1.93-2.71-13.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.994
r_dihedral_angle_4_deg15.821
r_dihedral_angle_3_deg14.811
r_dihedral_angle_1_deg6.683
r_long_range_B_refined6.173
r_long_range_B_other6.173
r_scangle_other4.918
r_scbond_it3.542
r_scbond_other3.542
r_mcangle_other2.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.994
r_dihedral_angle_4_deg15.821
r_dihedral_angle_3_deg14.811
r_dihedral_angle_1_deg6.683
r_long_range_B_refined6.173
r_long_range_B_other6.173
r_scangle_other4.918
r_scbond_it3.542
r_scbond_other3.542
r_mcangle_other2.93
r_mcangle_it2.927
r_mcbond_it2.373
r_mcbond_other2.367
r_angle_refined_deg1.747
r_angle_other_deg0.83
r_chiral_restr0.247
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_gen_planes_other0.001
r_bond_other_d
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 Atoms11718
Nucleic Acid Atoms
Solvent Atoms1493
Heterogen Atoms235

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing