2PID

Crystal structure of human mitochondrial tyrosyl-tRNA synthetase in complex with an adenylate analog


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VBMPDB ENTRY 1VBM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.52933 mg/ml protein, 30% (m/v) PEG 4000, 200 mM Ammonium acetate, 100 mM sodium acetate pH 4.6, 100 mM Tris-HCl pH 7.5, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.0540.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54α = 90
b = 62.4β = 90
c = 194.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 3152006-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.22099.50.0980.09819.111.834168-339.9
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)
12.22.31000.4270.4278.212.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1VBM2.219.983415634156170099.60.1930.1930.244RANDOM40.4
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]
7.63.12-10.72
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.7
c_scangle_it5.8
c_scbond_it4.2
c_mcangle_it3.84
c_mcbond_it2.83
c_improper_angle_d1.71
c_angle_deg1.4
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.7
c_scangle_it5.8
c_scbond_it4.2
c_mcangle_it3.84
c_mcbond_it2.83
c_improper_angle_d1.71
c_angle_deg1.4
c_bond_d0.008
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 Atoms5102
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms70

Software

Software
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing