2Z2K

Crystal structure of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PTHPDB ENTRY 2PTH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.529815%(w/v) PEG 8000, 100mm HEPES, 5%(v/v) 2-propanol, pH 7.5, Microbatch, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8132.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.84α = 90
b = 57.06β = 90
c = 72.59γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2006-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.493098.20.08215.144.1542837.8
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)
12.492.58950.3843.6522

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2PTH2.519.01539729998.30.1980.1980.241RANDOM35.6
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]
-11.3517.66-6.31
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.9
c_scangle_it2.94
c_mcangle_it2.19
c_scbond_it1.98
c_angle_deg1.4
c_mcbond_it1.33
c_improper_angle_d0.85
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1341
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms1

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing