3P2J

Crystal structure of peptidyl-tRNA hydrolase from Mycobacterium smegmatis at 2.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KJZPDB ENTRY 3KJZ

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
2.0239.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.909α = 90
b = 58.943β = 90
c = 61.854γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMARRESEARCHMIRROR2009-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.514

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
12.2242.6795.60.07811.98170817032.3
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)
12.222.389.40.6412

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 3KJZ2.2214.968170774437995.530.1930.192930.19160.21818RANDOM36.27
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]
0.59-0.41-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.979
r_dihedral_angle_4_deg17.788
r_dihedral_angle_3_deg16.984
r_scangle_it3.164
r_mcangle_it2.323
r_scbond_it1.973
r_angle_refined_deg1.707
r_dihedral_angle_1_deg1.602
r_mcbond_it1.296
r_chiral_restr0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.979
r_dihedral_angle_4_deg17.788
r_dihedral_angle_3_deg16.984
r_scangle_it3.164
r_mcangle_it2.323
r_scbond_it1.973
r_angle_refined_deg1.707
r_dihedral_angle_1_deg1.602
r_mcbond_it1.296
r_chiral_restr0.11
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1428
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling