6N9A

Crystal Structure of Thermotoga maritima threonylcarbamoyladenosine biosynthesis complex TsaB2D2E2 bound to ATP and carboxy-AMP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52932 uL sample solution containing 3.1 mg/mL protein, 50 mM Tris (pH 7.5), 50 mM NaCl, 1 mM ATP and 0.1 mM MgCl2 with 2 uL reservoir solution containing 8% polyethylene glycol (PEG) 400, 100 mM KCl, 50 mM MES (pH 6.0) and 0.8 mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.3863.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.053α = 90
b = 124.053β = 90
c = 119.035γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARMOSAIC 325 mm CCD2016-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL14-11.19499SSRLBL14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.5107.4398.80.1220.130.0426.1936821
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5484.21.8862.2971.2810.1822.6

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 REPLACEMENTTHROUGHOUT2A6A2.542.9431308178789.120.126810.121850.21438RANDOM76.982
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]
-1.66-0.83-1.665.38
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.744
r_sphericity_bonded43.476
r_dihedral_angle_2_deg33.739
r_dihedral_angle_3_deg17.962
r_long_range_B_refined17.051
r_long_range_B_other17.047
r_dihedral_angle_4_deg16.691
r_scangle_other16.523
r_mcangle_it13.933
r_mcangle_other13.932
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free47.744
r_sphericity_bonded43.476
r_dihedral_angle_2_deg33.739
r_dihedral_angle_3_deg17.962
r_long_range_B_refined17.051
r_long_range_B_other17.047
r_dihedral_angle_4_deg16.691
r_scangle_other16.523
r_mcangle_it13.933
r_mcangle_other13.932
r_scbond_it13.315
r_scbond_other13.305
r_mcbond_other10.643
r_mcbond_it10.64
r_dihedral_angle_1_deg6.934
r_rigid_bond_restr2.686
r_angle_refined_deg0.783
r_angle_other_deg0.77
r_chiral_restr0.04
r_bond_refined_d0.003
r_gen_planes_refined0.001
r_bond_other_d
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5490
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms105

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing