2NRE

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529820% PEG 3350, 0.2 M K3 Citrate, 5 mM spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5365.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.355α = 90
b = 80.355β = 90
c = 205.373γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102004-01-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.0ALS8.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
142099.20.1729.537.669986998
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
44.1497.90.5313.384.8664

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1DJ0 and 1EHZ4205809580932889.240.264620.264620.259460.35735RANDOM63.983
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]
0.710.360.71-1.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.65
r_dihedral_angle_3_deg21.798
r_dihedral_angle_4_deg20.92
r_dihedral_angle_1_deg6.097
r_mcangle_it1.378
r_angle_refined_deg1.327
r_mcbond_it0.762
r_scangle_it0.632
r_scbond_it0.374
r_xyhbond_nbd_refined0.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.65
r_dihedral_angle_3_deg21.798
r_dihedral_angle_4_deg20.92
r_dihedral_angle_1_deg6.097
r_mcangle_it1.378
r_angle_refined_deg1.327
r_mcbond_it0.762
r_scangle_it0.632
r_scbond_it0.374
r_xyhbond_nbd_refined0.34
r_nbtor_refined0.337
r_symmetry_hbond_refined0.325
r_nbd_refined0.308
r_symmetry_vdw_refined0.262
r_metal_ion_refined0.206
r_chiral_restr0.078
r_bond_refined_d0.012
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1961
Nucleic Acid Atoms1196
Solvent Atoms
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing