4QD3

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with 5-azacytidine at 1.89 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298PEG 4000, Isopropanol, HEPES buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2344.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.111α = 90
b = 64.111β = 90
c = 156.62γ = 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
11.8932.0899.90.07551.71607116071
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9299.90.4914.5

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 REPLACEMENTTHROUGHOUT4JC41.8932.081521279999.930.188970.186420.23803RANDOM28.774
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]
0.40.40.4-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.703
r_dihedral_angle_4_deg14.817
r_dihedral_angle_3_deg14.332
r_long_range_B_refined5.59
r_long_range_B_other5.586
r_dihedral_angle_1_deg4.884
r_angle_other_deg3.648
r_scangle_other2.577
r_mcangle_other2.05
r_mcangle_it2.049
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.703
r_dihedral_angle_4_deg14.817
r_dihedral_angle_3_deg14.332
r_long_range_B_refined5.59
r_long_range_B_other5.586
r_dihedral_angle_1_deg4.884
r_angle_other_deg3.648
r_scangle_other2.577
r_mcangle_other2.05
r_mcangle_it2.049
r_scbond_it1.55
r_scbond_other1.544
r_angle_refined_deg1.305
r_mcbond_it1.226
r_mcbond_other1.222
r_chiral_restr0.109
r_bond_refined_d0.014
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1467
Nucleic Acid Atoms
Solvent Atoms201
Heterogen Atoms23

Software

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