2J5B

Structure of the Tyrosyl tRNA synthetase from Acanthamoeba polyphaga Mimivirus complexed with tyrosynol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherLOW RESOLUTION MAD STRUCTURE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5RESERVOIR: 0.1 M SODIUM CITRATE BUFFER PH 5.5, PEG 4000 8% (W/V), 15% MPD (V/V), 0.1M KCL, 1MM MGCL2 DROPLET: 2 MICROL TYRRS 14 MG/ML IN 20 MM TRIS PH 7.4, 1MM TYROSINOL, 1MM ATP 0.5 MICROL RESERVOIR
Crystal Properties
Matthews coefficientSolvent content
3.1761.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.502α = 90
b = 107.3β = 90
c = 148.89γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210MIRROR2006-07-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.2871000.092.24.55253725.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.281000.292.34.6

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 REPLACEMENTTHROUGHOUTLOW RESOLUTION MAD STRUCTURE2.229.8352432264199.90.2160.2160.248RANDOM39
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]
-4.075.05-0.97
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.5
c_scangle_it3.48
c_scbond_it2.38
c_mcangle_it2.32
c_mcbond_it1.44
c_angle_deg1.1
c_improper_angle_d0.71
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.5
c_scangle_it3.48
c_scbond_it2.38
c_mcangle_it2.32
c_mcbond_it1.44
c_angle_deg1.1
c_improper_angle_d0.71
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5169
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms24

Software

Software
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing