2AJH

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


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 = 111.518α = 90
b = 111.518β = 90
c = 134.931γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IVosmic mirror2005-03-11MSINGLE 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
12.45098.90.1214.56.22000419784
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)
2.42.4999.70.4521.461941

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 REPLACEMENTTHROUGHOUT2.4201875518755100798.80.243310.243310.241080.28432RANDOM52.614
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]
2.331.172.33-3.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.149
r_scangle_it3.922
r_scbond_it2.408
r_mcangle_it1.583
r_angle_refined_deg1.474
r_mcbond_it0.815
r_nbd_refined0.23
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.149
r_scangle_it3.922
r_scbond_it2.408
r_mcangle_it1.583
r_angle_refined_deg1.474
r_mcbond_it0.815
r_nbd_refined0.23
r_symmetry_vdw_refined0.22
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.141
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.005
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 Atoms78
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
CNSphasing