3KFL

Leishmania major methionyl-tRNA synthetase in complex with methionyladenylate and pyrophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CSX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72982 microliters 24.44 mg/ml protein soln. [in 25 mM HEPES (pH 7.0), 500 mM NaCl, 0.025% Na-azide, 5% glycerol, 0.01 mM ZnCl2, 10 mM L-Met, 10 mM ATP] + 2 microliters well soln. [0.2 M K-formate, 26% PEG 3350 and additives of 10 mM L-Met and 1 mM TCEP]; crystal cryoprotected by quick soak in mother liquor supplemented with 15% ethylene glycol, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4349.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.816α = 90
b = 88.802β = 90
c = 101.779γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-04-23MSINGLE 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
12501000.0798.65.342546527.6
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)
22.071000.6991.85.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2csx237.1642461214199.70.170.170330.168260.20871RANDOM38.029
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]
-1.24.18-2.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.248
r_dihedral_angle_3_deg13.446
r_dihedral_angle_4_deg11.738
r_dihedral_angle_1_deg5.815
r_scangle_it4.297
r_scbond_it3.141
r_mcangle_it2.397
r_mcbond_it1.66
r_angle_refined_deg1.197
r_angle_other_deg0.849
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.248
r_dihedral_angle_3_deg13.446
r_dihedral_angle_4_deg11.738
r_dihedral_angle_1_deg5.815
r_scangle_it4.297
r_scbond_it3.141
r_mcangle_it2.397
r_mcbond_it1.66
r_angle_refined_deg1.197
r_angle_other_deg0.849
r_mcbond_other0.561
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4240
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms82

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
BALBESphasing