5XOB

Crystal structure of apo TiaS (tRNAIle2 agmatidine synthetase)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP28950mM HEPES-Na pH7.0-7.2, 0.5M NH4Ac, 0.2M MgCl2, 1.5-2.5% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.6653.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.926α = 90
b = 68.926β = 90
c = 211.102γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDMARMOSAIC 325 mm CCD2010-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17B10.979SSRFBL17B1

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
12.475099.121.311.618539

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT2.4849.291841496298.020.245180.244650.29439RANDOM83.054
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]
3.853.85-7.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.554
r_dihedral_angle_4_deg19.92
r_dihedral_angle_3_deg19.519
r_long_range_B_refined8.479
r_long_range_B_other8.478
r_dihedral_angle_1_deg6.897
r_scangle_other5.714
r_mcangle_it5.237
r_mcangle_other5.236
r_scbond_it3.258
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.554
r_dihedral_angle_4_deg19.92
r_dihedral_angle_3_deg19.519
r_long_range_B_refined8.479
r_long_range_B_other8.478
r_dihedral_angle_1_deg6.897
r_scangle_other5.714
r_mcangle_it5.237
r_mcangle_other5.236
r_scbond_it3.258
r_scbond_other3.258
r_mcbond_it3.09
r_mcbond_other3.089
r_angle_refined_deg1.224
r_angle_other_deg0.741
r_chiral_restr0.067
r_bond_refined_d0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3282
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing