2XGT

Asparaginyl-tRNA synthetase from Brugia malayi complexed with the sulphamoyl analogue of asparaginyl-adenylate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherT. THERMOPHILUS ASPARAGINYL-TRNA SYNTHETASE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5100MM HEPES PH8.5, 200MM NA-ACETATE, 14-16% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5652

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.51α = 90
b = 125.7β = 90
c = 144.268γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2000-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.93089.50.0914.93.971529
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)
11.9269.60.441.92.3

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 REPLACEMENTTHROUGHOUTT. THERMOPHILUS ASPARAGINYL-TRNA SYNTHETASE1.994.9269345213688.880.203780.202310.25017RANDOM17.042
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]
-0.731.44-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.669
r_dihedral_angle_4_deg15.827
r_dihedral_angle_3_deg14.695
r_dihedral_angle_1_deg6.26
r_scangle_it2.914
r_scbond_it1.825
r_angle_refined_deg1.325
r_mcangle_it1.261
r_angle_other_deg0.898
r_mcbond_it0.692
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.669
r_dihedral_angle_4_deg15.827
r_dihedral_angle_3_deg14.695
r_dihedral_angle_1_deg6.26
r_scangle_it2.914
r_scbond_it1.825
r_angle_refined_deg1.325
r_mcangle_it1.261
r_angle_other_deg0.898
r_mcbond_it0.692
r_mcbond_other0.154
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms6960
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing