2XTI

Asparaginyl-tRNA synthetase from Brugia malayi complexed with ATP:Mg and L-Asp-beta-NOH adenylate:PPi:Mg


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XGTPDB ENTRY 2XGT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5ROOM TEMPERATURE HANGING-DROP VAPOUR DIFFUSION IN 0.1 M HEPES PH 8.5, 200MM SODIUM ACETATE USING 17-19 % PEG 4000 AS PRECIPITANT. PROTEIN CONCENTRATION OF 2.5MG/ML WITH 10 MM ATP:MGCL2, 10 MM L-ASP-BETA-NOH.
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.92α = 90
b = 106.39β = 90
c = 161.42γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2003-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
12.45097.60.1103.638929
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)
12.42.4995.40.423.33.7

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 2XGT2.448.223737115581000.216060.212780.29837RANDOM29.6
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]
5.48-1.59-3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.885
r_dihedral_angle_4_deg16.574
r_dihedral_angle_3_deg16.024
r_dihedral_angle_1_deg6.341
r_scangle_it2.064
r_angle_refined_deg1.356
r_scbond_it1.318
r_mcangle_it0.894
r_angle_other_deg0.863
r_mcbond_it0.493
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.885
r_dihedral_angle_4_deg16.574
r_dihedral_angle_3_deg16.024
r_dihedral_angle_1_deg6.341
r_scangle_it2.064
r_angle_refined_deg1.356
r_scbond_it1.318
r_mcangle_it0.894
r_angle_other_deg0.863
r_mcbond_it0.493
r_mcbond_other0.098
r_chiral_restr0.078
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6968
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing