4RRL

E129A mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Ser3AA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.1M Tris HCl pH 8.5, 0.2M MgCl2, 30% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0640.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.023α = 90
b = 47.023β = 90
c = 112.514γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2012-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.962597.49189895022

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.96524.8929189895045498.060.187160.184790.23579RANDOM36.14
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]
0.330.33-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.693
r_dihedral_angle_3_deg17.124
r_dihedral_angle_4_deg14.33
r_dihedral_angle_1_deg6.722
r_angle_refined_deg1.656
r_chiral_restr0.118
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.693
r_dihedral_angle_3_deg17.124
r_dihedral_angle_4_deg14.33
r_dihedral_angle_1_deg6.722
r_angle_refined_deg1.656
r_chiral_restr0.118
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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 Atoms1060
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms25

Software

Software
Software NamePurpose
AUTOMARdata collection
MOLREPphasing
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling