2AJI

Crystal structure of the editing domain of E. coli leucyl-tRNA synthetase complexes with isoleucine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293(NH4)2SO4, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.487α = 90
b = 112.487β = 90
c = 135.023γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IVosmic mirror2005-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
13.25089.40.0918.74.486427726
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)
3.23.3789.40.412.14.41086

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.2207329732936387.820.234360.234360.231960.2836RANDOM55.124
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]
2.211.12.21-3.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.103
r_scangle_it2.039
r_angle_refined_deg1.17
r_scbond_it1.105
r_mcangle_it0.99
r_mcbond_it0.522
r_symmetry_vdw_refined0.234
r_nbd_refined0.219
r_xyhbond_nbd_refined0.135
r_symmetry_hbond_refined0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.103
r_scangle_it2.039
r_angle_refined_deg1.17
r_scbond_it1.105
r_mcangle_it0.99
r_mcbond_it0.522
r_symmetry_vdw_refined0.234
r_nbd_refined0.219
r_xyhbond_nbd_refined0.135
r_symmetry_hbond_refined0.127
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2693
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
CNSphasing