1E1O

lysyl-tRNA Synthetase (LYSU) hexagonal form, complexed with lysine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8PROTEIN WAS CRYSTALLISED FROM 0.1M PIPES PH 6.8, 0.5 M LICL; 20% PEG 4K, 17% GLYCEROL
Crystal Properties
Matthews coefficientSolvent content
4.874

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.1α = 90
b = 143.1β = 90
c = 176.1γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRROR1995-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
12.122599.60.0850.0858.816.260434
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)
12.122.1699.60.260.263.715.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1LYL2.122057124230199.60.1950.1950.233RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.7
x_scangle_it6.41
x_scbond_it4.11
x_mcangle_it3.36
x_mcbond_it2.13
x_angle_deg1.6
x_improper_angle_d1.17
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d23.7
x_scangle_it6.41
x_scbond_it4.11
x_mcangle_it3.36
x_mcbond_it2.13
x_angle_deg1.6
x_improper_angle_d1.17
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3815
Nucleic Acid Atoms
Solvent Atoms361
Heterogen Atoms58

Software

Software
Software NamePurpose
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
X-PLORphasing