3HRK

Histidyl-tRNA synthetase from Trypanosoma cruzi (Histidyl-adenylate complex)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HRJPDB ENTRY 3HRJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.52930.2 M Lithium Sulfate, 28% PEG 3350, 0.1 M Bis/Tris pH 5.5, 1mM TCEP, 10 mM L-Histidine; subsequent soak against effective concentration 5mM ATP, 5mM MgCl2, vapor diffusion, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0359.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.36α = 90
b = 166.987β = 90
c = 66.021γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-04-22SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97923SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
13.055080.30.127.74631959963
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.053.1668.70.9052.71641

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 3HRJ3.0542.5619569102280.230.2360.2320.308RANDOM29.905
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]
-0.935.67-4.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.036
r_dihedral_angle_3_deg16.497
r_dihedral_angle_4_deg14.111
r_dihedral_angle_1_deg6.072
r_scangle_it1.488
r_angle_refined_deg1.119
r_scbond_it0.824
r_angle_other_deg0.803
r_mcangle_it0.69
r_mcbond_it0.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.036
r_dihedral_angle_3_deg16.497
r_dihedral_angle_4_deg14.111
r_dihedral_angle_1_deg6.072
r_scangle_it1.488
r_angle_refined_deg1.119
r_scbond_it0.824
r_angle_other_deg0.803
r_mcangle_it0.69
r_mcbond_it0.363
r_chiral_restr0.056
r_mcbond_other0.045
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6477
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms67

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling