1E1T

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH THE LYSYL_ADENYLATE INTERMEDIATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E1OPDB ENTRY 1E1O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION CONTAINING ATP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM.
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 X11EMBL/DESY, HAMBURGX11

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
12.41598.20.0860.08610.5841908
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)
12.42.4494.10.2040.2044.13.6

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 1E1O2.415408601639980.1860.1860.267RANDOM
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_d17
x_scangle_it6.3
x_scbond_it4.2
x_mcangle_it3.4
x_mcbond_it2.26
x_improper_angle_d1.66
x_angle_deg1.6
x_bond_d0.007
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d17
x_scangle_it6.3
x_scbond_it4.2
x_mcangle_it3.4
x_mcbond_it2.26
x_improper_angle_d1.66
x_angle_deg1.6
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 Atoms3834
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms85

Software

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