1X55

Crystal structure of asparaginyl-tRNA synthetase from Pyrococcus horikoshii complexed with asparaginyl-adenylate analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B8APDB ENTRY 1B8A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293PEG8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.957.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.212α = 90
b = 68.024β = 117.35
c = 75.604γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102004-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.85095.94.75272850566-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8677.43.5

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 1B8A1.830.334803525290.174750.173480.19855RANDOM19.086
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]
-0.54-0.641.28-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.706
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg13.392
r_dihedral_angle_1_deg6.011
r_scangle_it3.36
r_scbond_it2.268
r_angle_refined_deg1.374
r_mcangle_it1.35
r_mcbond_it0.885
r_nbd_refined0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.706
r_dihedral_angle_4_deg15.725
r_dihedral_angle_3_deg13.392
r_dihedral_angle_1_deg6.011
r_scangle_it3.36
r_scbond_it2.268
r_angle_refined_deg1.374
r_mcangle_it1.35
r_mcbond_it0.885
r_nbd_refined0.2
r_xyhbond_nbd_refined0.164
r_symmetry_hbond_refined0.155
r_symmetry_vdw_refined0.147
r_chiral_restr0.099
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3544
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing