X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P0H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2771:1:0.5 native protein solution (14 mg/ml LmTyrRS in MSGPP buffer containing 1 mM TCEP and 10 mM tyrosinol): well solutionn (16% PEG 3350, 0.2 M potassium formate pH 7.5): seed stock (1:100 dilution in SGPP buffer); cryoprotected by quick soak in 15% ethylene glycol, 18.75% PEG 3350, 187.5 mM potassium formate pH 7.5, 10mM tyrosinol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.7955.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.519α = 74.47
b = 111.934β = 80.83
c = 141.043γ = 77.13
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2009-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
12.89135.1398.60.08414.1183.672441-376
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.89397.91.0633.5

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 REPLACEMENTTHROUGHOUT3P0H2.895072441364998.070.24620.24380.293RANDOM143.308
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]
3.68-2.29-0.71-1.740.89-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.782
r_dihedral_angle_3_deg17.15
r_dihedral_angle_4_deg14.571
r_dihedral_angle_1_deg5.413
r_angle_refined_deg1.05
r_angle_other_deg0.809
r_chiral_restr0.057
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.782
r_dihedral_angle_3_deg17.15
r_dihedral_angle_4_deg14.571
r_dihedral_angle_1_deg5.413
r_angle_refined_deg1.05
r_angle_other_deg0.809
r_chiral_restr0.057
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19644
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms50

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling