1SGV

STRUCTURE OF TRNA PSI55 PSEUDOURIDINE SYNTHASE (TRUB)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microseeding7.5298AMMONIUM SULFATE, TRIS BUFFER, PEG3350, pH 7.5, temperature 298K, microseeding
Crystal Properties
Matthews coefficientSolvent content
3.0359.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.948α = 90
b = 94.1β = 100.36
c = 78.508γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.11.0322ALS5.0.1

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
11.940.20.04612.43.65141128.8
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)
11.91.970.3423.2

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 REPLACEMENTTHROUGHOUTPDB entry 1K8W protein component1.940.1648859255199.430.202680.200820.23947RANDOM20.756
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]
-0.040.35-0.430.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.461
r_scangle_it2.258
r_scbond_it1.254
r_angle_refined_deg0.973
r_mcangle_it0.749
r_mcbond_it0.387
r_symmetry_vdw_refined0.191
r_nbd_refined0.183
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.461
r_scangle_it2.258
r_scbond_it1.254
r_angle_refined_deg0.973
r_mcangle_it0.749
r_mcbond_it0.387
r_symmetry_vdw_refined0.191
r_nbd_refined0.183
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.127
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3930
Nucleic Acid Atoms
Solvent Atoms451
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing