2V0C | pdb_00002v0c

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H3NPDB ENTRY 1H3N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PROTEIN 10 MG/ML IN 50MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5 2MM DTT, 20MM MGCL2, 1MM NAN3, 18% AMMONIUM SULPHATE EQUILBRIATED AGAINST 30-38% AMMONIUM SULPHATE IN 100MM BIS-TRIS PROPANE BUFFER PH 6.0-6.5.
Crystal Properties
Matthews coefficientSolvent content
3.564.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.83α = 90
b = 154.23β = 90
c = 174.95γ = 90
Symmetry
Space GroupC 2 2 21

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
11.855099.30.0613.864.1472672
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)
11.851.991.20.552.423.7

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 1H3N1.8587.37112717347799.50.1810.180.190.2020.21RANDOM21.12
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]
-0.160.85-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.152
r_dihedral_angle_4_deg19.74
r_dihedral_angle_3_deg12.839
r_dihedral_angle_1_deg6.04
r_scangle_it3.369
r_scbond_it2.341
r_angle_refined_deg1.494
r_mcangle_it1.375
r_mcbond_it1.295
r_angle_other_deg0.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.152
r_dihedral_angle_4_deg19.74
r_dihedral_angle_3_deg12.839
r_dihedral_angle_1_deg6.04
r_scangle_it3.369
r_scbond_it2.341
r_angle_refined_deg1.494
r_mcangle_it1.375
r_mcbond_it1.295
r_angle_other_deg0.94
r_symmetry_vdw_other0.34
r_nbd_refined0.211
r_nbd_other0.197
r_nbtor_refined0.181
r_symmetry_hbond_refined0.17
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.152
r_chiral_restr0.106
r_nbtor_other0.085
r_bond_refined_d0.014
r_gen_planes_refined0.006
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 Atoms6608
Nucleic Acid Atoms
Solvent Atoms684
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing