5ZX8

Crystal structure of peptidyl-tRNA hydrolase from Thermus thermophilus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2293100 mM phosphate-citrate buffer pH 4.2, 50%(v/v) 2-methyl-2,4-pentanediol
Crystal Properties
Matthews coefficientSolvent content
1.8232.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.453α = 90
b = 53.918β = 90
c = 58.67γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2102010-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.000Photon FactoryAR-NW12A

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
115092.60.04557.27.975984
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)
111.040.46

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 REPLACEMENTTHROUGHOUT1RYB123.4571946377792.250.129380.128670.14272RANDOM16.198
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]
-0.590.280.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.514
r_sphericity_free25.636
r_dihedral_angle_4_deg17.386
r_dihedral_angle_3_deg14.311
r_sphericity_bonded10.507
r_dihedral_angle_1_deg6.297
r_long_range_B_refined4.079
r_rigid_bond_restr4.074
r_scangle_other4.043
r_scbond_it3.971
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.514
r_sphericity_free25.636
r_dihedral_angle_4_deg17.386
r_dihedral_angle_3_deg14.311
r_sphericity_bonded10.507
r_dihedral_angle_1_deg6.297
r_long_range_B_refined4.079
r_rigid_bond_restr4.074
r_scangle_other4.043
r_scbond_it3.971
r_scbond_other3.969
r_long_range_B_other3.899
r_angle_refined_deg1.874
r_mcangle_other1.601
r_mcangle_it1.556
r_mcbond_it1.351
r_mcbond_other1.179
r_angle_other_deg0.906
r_chiral_restr0.429
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1448
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing