5U21

X-ray structure of the WlaRF aminotransferase from Campylobacter jejuni, K184A mutant in complex with TDP-Qui3N


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 (pH 7) 12-15% PEG-3350 1 mM PLP 10 mM TDP-Qui3N
Crystal Properties
Matthews coefficientSolvent content
2.1743.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.164α = 90
b = 56.653β = 90.04
c = 124.802γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-08-21MSINGLE 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
11.65097.60.0650.06510.23194888
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)
11.61.792.70.3031.91.9

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 REPLACEMENTTHROUGHOUT5u1z1.629.98185140973897.410.133690.132220.16132RANDOM16.422
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]
7.16-3.350.49-7.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.728
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg13.88
r_dihedral_angle_1_deg6.857
r_long_range_B_refined5.615
r_long_range_B_other5.615
r_scangle_other4.254
r_scbond_it3.002
r_scbond_other3.001
r_mcangle_it2.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.728
r_dihedral_angle_4_deg15.202
r_dihedral_angle_3_deg13.88
r_dihedral_angle_1_deg6.857
r_long_range_B_refined5.615
r_long_range_B_other5.615
r_scangle_other4.254
r_scbond_it3.002
r_scbond_other3.001
r_mcangle_it2.586
r_mcangle_other2.586
r_mcbond_it2.05
r_mcbond_other2.049
r_angle_refined_deg1.829
r_angle_other_deg0.855
r_chiral_restr0.12
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms11714
Nucleic Acid Atoms
Solvent Atoms1594
Heterogen Atoms227

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing