2JJQ

The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
115% PEG 8000, 0.05 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE PH 5.6
Crystal Properties
Matthews coefficientSolvent content
1.9937.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.894α = 90
b = 63.313β = 90
c = 101.685γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.93099.70.07225.2330082
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)
11.91.9398.50.483.74.9

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 REPLACEMENTTHROUGHOUT1.853.7636427192199.90.1850.1820.228RANDOM24.48
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]
-0.130.85-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.731
r_dihedral_angle_4_deg20.276
r_dihedral_angle_3_deg13.625
r_dihedral_angle_1_deg6.026
r_scangle_it5.639
r_scbond_it3.392
r_mcangle_it2.042
r_angle_refined_deg1.713
r_mcbond_it1.099
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.731
r_dihedral_angle_4_deg20.276
r_dihedral_angle_3_deg13.625
r_dihedral_angle_1_deg6.026
r_scangle_it5.639
r_scbond_it3.392
r_mcangle_it2.042
r_angle_refined_deg1.713
r_mcbond_it1.099
r_chiral_restr0.138
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
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_mcbond_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 Atoms3216
Nucleic Acid Atoms
Solvent Atoms384
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing