2WFD

Structure of the human cytosolic leucyl-tRNA synthetase editing domain


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.2 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 8.3, 20% W/V POLYETHYLENE GLYCOL 3350
Crystal Properties
Matthews coefficientSolvent content
3.4563.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.54α = 90
b = 94.54β = 90
c = 148.82γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
133099.80.157.463.1215008
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)
13.253.399.50.661.983.16

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 DIFFRACTIONSADTHROUGHOUTNONE3.2529.24111986121000.2040.2020.24RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.273
r_dihedral_angle_3_deg17.806
r_dihedral_angle_4_deg17.321
r_dihedral_angle_1_deg6.816
r_scangle_it1.571
r_angle_refined_deg1.318
r_scbond_it0.943
r_angle_other_deg0.852
r_mcangle_it0.65
r_mcbond_it0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.273
r_dihedral_angle_3_deg17.806
r_dihedral_angle_4_deg17.321
r_dihedral_angle_1_deg6.816
r_scangle_it1.571
r_angle_refined_deg1.318
r_scbond_it0.943
r_angle_other_deg0.852
r_mcangle_it0.65
r_mcbond_it0.336
r_chiral_restr0.069
r_mcbond_other0.043
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_mcangle_other
r_scbond_other
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 Atoms3922
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDphasing