4QBK

Crystal structure of the complex of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with amino acyl-tRNA analogue at 1.77 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JC4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52980.1M HEPES buffer, PEG 4000, 5% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2946.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.751α = 90
b = 64.751β = 90
c = 157.679γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2013-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

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
11.7727.621000.0622519890
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.771.81002.1

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 REPLACEMENTTHROUGHOUT4JC41.7727.6218884101699.940.174650.174190.18323RANDOM27.116
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]
0.250.130.25-0.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.467
r_dihedral_angle_3_deg15.122
r_dihedral_angle_4_deg11.112
r_long_range_B_other6.5
r_long_range_B_refined6.497
r_dihedral_angle_1_deg4.991
r_angle_other_deg3.647
r_scangle_other3.542
r_mcangle_it2.361
r_mcangle_other2.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.467
r_dihedral_angle_3_deg15.122
r_dihedral_angle_4_deg11.112
r_long_range_B_other6.5
r_long_range_B_refined6.497
r_dihedral_angle_1_deg4.991
r_angle_other_deg3.647
r_scangle_other3.542
r_mcangle_it2.361
r_mcangle_other2.361
r_scbond_it2.171
r_scbond_other2.17
r_angle_refined_deg1.668
r_mcbond_it1.479
r_mcbond_other1.477
r_chiral_restr0.109
r_bond_refined_d0.018
r_gen_planes_other0.008
r_gen_planes_refined0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1467
Nucleic Acid Atoms
Solvent Atoms219
Heterogen Atoms38

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling