3WO1

Crystal structure of Trp332Ala mutant YwfE, an L-amino acid ligase, with bound ADP-Mg-Ala


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2529316% PEG 3350, 0.3M NaCl, 0.1M HEPES-NaOH, 5% ethylene glycol, 1mM DTT, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.129α = 90
b = 91.129β = 90
c = 258.757γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2013-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-NW12A

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
12.32098.10.03855.67.628700
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)
12.32.351000.3227.67.71799

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 DIFFRACTIONSADTHROUGHOUT2.319.7427089147597.620.223560.221450.26141RANDOM73.943
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]
-2.41-2.41-2.417.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.446
r_dihedral_angle_4_deg17.345
r_dihedral_angle_3_deg17.302
r_dihedral_angle_1_deg7.862
r_angle_refined_deg1.344
r_angle_other_deg0.692
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.446
r_dihedral_angle_4_deg17.345
r_dihedral_angle_3_deg17.302
r_dihedral_angle_1_deg7.862
r_angle_refined_deg1.344
r_angle_other_deg0.692
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms3623
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms35

Software

Software
Software NamePurpose
HKL-2000data collection
CRANKphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling