4QT4

Crystal structure of Peptidyl-tRNA hydrolase from a Gram-positive bacterium, Streptococcus pyogenes at 2.19 Angstrom resolution shows the Closed Structure of the Substrate Binding Cleft


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPVAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.141.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.024α = 90.33
b = 43.028β = 105.78
c = 65.1γ = 112.51
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCHMirror2013-11-26MSINGLE 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
12.1935.3798.30.06222.217325
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)
12.192.2397.30.1577.6

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 REPLACEMENTTHROUGHOUT4JC42.1935.371643988497.880.170020.168440.19847RANDOM17.196
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]
1.140.150.51-0.410.06-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.965
r_dihedral_angle_4_deg20.031
r_dihedral_angle_3_deg17.583
r_angle_other_deg3.602
r_dihedral_angle_1_deg3.221
r_mcangle_it1.687
r_mcangle_other1.687
r_angle_refined_deg1.589
r_mcbond_it1.066
r_mcbond_other1.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.965
r_dihedral_angle_4_deg20.031
r_dihedral_angle_3_deg17.583
r_angle_other_deg3.602
r_dihedral_angle_1_deg3.221
r_mcangle_it1.687
r_mcangle_other1.687
r_angle_refined_deg1.589
r_mcbond_it1.066
r_mcbond_other1.064
r_chiral_restr0.137
r_bond_refined_d0.014
r_gen_planes_other0.009
r_gen_planes_refined0.006
r_bond_other_d
r_scbond_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2978
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms

Software

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