4RDI

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529525% (w/v) PEG 3350, 0.1 M Tris, pH 8.5 and 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9938.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.71α = 90
b = 97.036β = 111.83
c = 84.215γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.97933PAL/PLS5C (4A)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.955098.60.0820.0823.770428
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9897.40.3620.3624.813.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.955066826354598.490.158970.156310.20916RANDOM26.35
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]
-1.01-0.550.081.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.617
r_dihedral_angle_4_deg18.201
r_dihedral_angle_3_deg16.201
r_long_range_B_refined7.446
r_long_range_B_other7.065
r_dihedral_angle_1_deg5.803
r_scangle_other5.017
r_mcangle_it3.409
r_mcangle_other3.409
r_scbond_it3.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.617
r_dihedral_angle_4_deg18.201
r_dihedral_angle_3_deg16.201
r_long_range_B_refined7.446
r_long_range_B_other7.065
r_dihedral_angle_1_deg5.803
r_scangle_other5.017
r_mcangle_it3.409
r_mcangle_other3.409
r_scbond_it3.393
r_scbond_other3.392
r_mcbond_it2.405
r_mcbond_other2.405
r_angle_refined_deg2.028
r_angle_other_deg0.895
r_chiral_restr0.116
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms7286
Nucleic Acid Atoms
Solvent Atoms610
Heterogen Atoms148

Software

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