5Y98

Crystal structure of native unbound peptidyl tRNA hydrolase from Acinetobacter baumannii at 1.36 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WH4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529850mM HEPES, PEG 400, PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
238.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.98α = 90
b = 65.97β = 90
c = 75.88γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirror2013-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.3625.3299.920.24.237477
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.361.395

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 REPLACEMENTTHROUGHOUT3WH41.3625.3235544187199.930.108070.106210.14449RANDOM14.678
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.582
r_dihedral_angle_2_deg34.793
r_dihedral_angle_4_deg14.868
r_sphericity_bonded13.731
r_dihedral_angle_3_deg12.882
r_rigid_bond_restr9.097
r_long_range_B_refined7.279
r_long_range_B_other7.069
r_dihedral_angle_1_deg5.9
r_mcangle_it5.497
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free39.582
r_dihedral_angle_2_deg34.793
r_dihedral_angle_4_deg14.868
r_sphericity_bonded13.731
r_dihedral_angle_3_deg12.882
r_rigid_bond_restr9.097
r_long_range_B_refined7.279
r_long_range_B_other7.069
r_dihedral_angle_1_deg5.9
r_mcangle_it5.497
r_mcangle_other5.495
r_scangle_other5.049
r_scbond_other4.289
r_scbond_it4.288
r_mcbond_other3.964
r_mcbond_it3.96
r_angle_other_deg2.799
r_angle_refined_deg2.21
r_chiral_restr0.157
r_bond_refined_d0.031
r_gen_planes_other0.013
r_gen_planes_refined0.012
r_bond_other_d0.002
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 Atoms1496
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms6

Software

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