5XAQ

Crystal structure of Animalia-specific tRNA deacylase from Mus musculus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277BICINE (pH 8.0), PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.3246.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.379α = 90
b = 75.351β = 90
c = 103.619γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2016-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54179

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
11.8660.9489.50.07621.86.429268
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)
11.861.9351.20.382.43.7

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 REPLACEMENTFREE R-VALUE4NBI1.8660.9424840126289.560.203570.201210.24967RANDOM31.403
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]
2.43-0.45-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.558
r_dihedral_angle_3_deg15.617
r_dihedral_angle_4_deg13.133
r_dihedral_angle_1_deg7.583
r_long_range_B_refined7.349
r_long_range_B_other7.309
r_scangle_other5.983
r_scbond_it3.978
r_scbond_other3.977
r_mcangle_it3.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.558
r_dihedral_angle_3_deg15.617
r_dihedral_angle_4_deg13.133
r_dihedral_angle_1_deg7.583
r_long_range_B_refined7.349
r_long_range_B_other7.309
r_scangle_other5.983
r_scbond_it3.978
r_scbond_other3.977
r_mcangle_it3.619
r_mcangle_other3.618
r_mcbond_it2.88
r_mcbond_other2.88
r_angle_refined_deg2.041
r_angle_other_deg1.087
r_chiral_restr0.133
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2500
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms

Software

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