2V0G | pdb_00002v0g

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A tRNA(leu) transcript with 5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1- BENZOXABOROLE (AN2690) forming an adduct to the ribose of adenosine- 76 in the enzyme editing site.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BYTPDB ENTRY 2BYT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15MG/ML LEUCYL-TRNA SYNTHETASE, MOLAR RATIO PROTEIN:TRNA 1.0:1.2 5MM L-LEUCINE, 15MM MGCL2, 50MM MES PH6.5, 0.8M AMMONIUM SULPHATE AGAINST RESERVOIR CONTAINING 1.5M AMMONIUM SULPHATE AND 0.1M MES PH6.5
Crystal Properties
Matthews coefficientSolvent content
3.968

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 202.05α = 90
b = 125.8β = 118.71
c = 173.2γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
13.55094.90.1293138057
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)
13.53.696.80.452.692.95

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2BYT3.5152.543437232495.10.2490.2450.230.3140.29RANDOM66.29
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]
12.087.82-4.06-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.067
r_dihedral_angle_3_deg18.442
r_dihedral_angle_4_deg15.456
r_dihedral_angle_1_deg6.516
r_scangle_it1.349
r_angle_refined_deg1.335
r_angle_other_deg0.873
r_mcangle_it0.715
r_scbond_it0.682
r_mcbond_it0.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.067
r_dihedral_angle_3_deg18.442
r_dihedral_angle_4_deg15.456
r_dihedral_angle_1_deg6.516
r_scangle_it1.349
r_angle_refined_deg1.335
r_angle_other_deg0.873
r_mcangle_it0.715
r_scbond_it0.682
r_mcbond_it0.669
r_nbd_refined0.212
r_nbtor_refined0.197
r_nbd_other0.187
r_xyhbond_nbd_refined0.175
r_symmetry_vdw_other0.161
r_symmetry_hbond_refined0.12
r_symmetry_vdw_refined0.116
r_nbtor_other0.085
r_chiral_restr0.079
r_bond_refined_d0.01
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14244
Nucleic Acid Atoms3286
Solvent Atoms
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing