5UJJ

Crystal structure of human H130R tryptophanyl-tRNA synthetase in complex with TrpAMP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527718% PEG1500, 0.1mol/L Bis-Tris pH6.5
Crystal Properties
Matthews coefficientSolvent content
2.3146.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.352α = 90
b = 95.277β = 130.46
c = 99.623γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.987SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.175.899.20.0570.0498.56.956074
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1499.60.170.15972837

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 REPLACEMENTTHROUGHOUT2QUI2.15053339273599.10.21630.21550.2319RANDOM23.093
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]
0.47-0.09-0.430.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.17
r_dihedral_angle_3_deg13.249
r_dihedral_angle_4_deg11.755
r_dihedral_angle_1_deg5.817
r_angle_refined_deg1.113
r_angle_other_deg0.876
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.17
r_dihedral_angle_3_deg13.249
r_dihedral_angle_4_deg11.755
r_dihedral_angle_1_deg5.817
r_angle_refined_deg1.113
r_angle_other_deg0.876
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6711
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms77

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing