5OMW

Mutant T252A of E. coli leucyl-tRNA synthetase, tRNA(leu) and leucyl-adenylate analogue in the aminoacylation conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AQ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.1 M BIS-TRIS PH 5.5, 23-25% W/V PEG 3350, AND 200 MM AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.3647.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.25α = 90
b = 68.91β = 104.93
c = 228.33γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.6220.6299.80.1210.9927.83.573538
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6999.90.7630.661.53.69

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 REPLACEMENTTHROUGHOUT4AQ72.6220.6269873366599.80.220920.218670.26416RANDOM59.569
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]
0.280.240.37-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.231
r_dihedral_angle_3_deg15.271
r_dihedral_angle_4_deg14.593
r_dihedral_angle_1_deg5.673
r_long_range_B_refined5.177
r_long_range_B_other5.177
r_mcangle_it3.622
r_mcangle_other3.622
r_scangle_other3.174
r_mcbond_it2.092
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.231
r_dihedral_angle_3_deg15.271
r_dihedral_angle_4_deg14.593
r_dihedral_angle_1_deg5.673
r_long_range_B_refined5.177
r_long_range_B_other5.177
r_mcangle_it3.622
r_mcangle_other3.622
r_scangle_other3.174
r_mcbond_it2.092
r_mcbond_other2.092
r_scbond_it1.868
r_scbond_other1.868
r_angle_refined_deg1.131
r_angle_other_deg0.973
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms13666
Nucleic Acid Atoms3409
Solvent Atoms
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing