1E22

LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM complexed with lysine and the non-hydrolysable atp analogue amp-pcp


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5 MM 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 AMP-PCP 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 = 142.02α = 90
b = 142.02β = 90
c = 175.39γ = 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
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

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
12.432584.70.0650.0658.13.633781
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)
12.432.5465.10.0990.0996.33.1

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 REPLACEMENTTHROUGHOUT1E1O2.431233420134784.70.1760.1760.228RANDOM
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_d20.4
x_scangle_it6.9
x_scbond_it4.52
x_mcangle_it3.66
x_improper_angle_d2.4
x_mcbond_it2.39
x_angle_deg1.4
x_bond_d0.006
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d20.4
x_scangle_it6.9
x_scbond_it4.52
x_mcangle_it3.66
x_improper_angle_d2.4
x_mcbond_it2.39
x_angle_deg1.4
x_bond_d0.006
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 Atoms3816
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms80

Software

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