3KJZ

Crystal structure of native peptidyl-tRNA hydrolase from Mycobacterium smegmatis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z2IPDB ENTRY 2Z2I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529820mM Tris-HCl, 1mM EDTA, 50mM NaCl, 10% isopropanol, 30% PEG 1500, 5mM 2-mercaptoethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0339.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.01α = 90
b = 58.98β = 90
c = 62.02γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray291IMAGE PLATEMAR scanner 345 mm plateMirror2009-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.54

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
12.423.43956520650135.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.597.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Z2I2.423.436520650136295.30.190.1820.1820.221RANDOM32.5
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]
1.7-2.070.37
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it5.21
c_mcangle_it4.27
c_scbond_it3.75
c_mcbond_it2.79
c_angle_deg1.6
c_improper_angle_d0.91
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it5.21
c_mcangle_it4.27
c_scbond_it3.75
c_mcbond_it2.79
c_angle_deg1.6
c_improper_angle_d0.91
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1428
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling