4JC4

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa at 2.25 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529825% w/v PEG 4000, 5% isopropanol, 100mM HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.604α = 90
b = 62.604β = 90
c = 155.392γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMIRROR2012-05-20MSINGLE 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
12.2554.2298.70.071611516115
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3388.73.8

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 REPLACEMENTTHROUGHOUT4DHW2.2554.221611547998.660.186560.184950.21738RANDOM30.55
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]
0.350.350.35-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.088
r_dihedral_angle_4_deg20.205
r_dihedral_angle_3_deg17.642
r_dihedral_angle_1_deg6.113
r_angle_other_deg3.685
r_angle_refined_deg1.949
r_chiral_restr0.147
r_bond_refined_d0.027
r_gen_planes_other0.018
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1467
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms6

Software

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