5AGS

Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct 3-(Aminomethyl)-4-bromo-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AJGPDB ENTRY 2AJG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.50.1 M BIS-TRIS PH 5.5, 17% W/V PEG 10000, 0.2 M AMMONIUM ACETATE
Crystal Properties
Matthews coefficientSolvent content
2.242.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.75α = 90
b = 62.16β = 90
c = 76.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.4738.799.40.0617.24.3351802
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)
11.471.5198.40.812.34

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2AJG1.4738.6935180185799.380.184590.183390.2064RANDOM16.287
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]
0.690.27-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.589
r_dihedral_angle_4_deg13.057
r_dihedral_angle_3_deg12.828
r_dihedral_angle_1_deg5.967
r_scangle_it2.722
r_scbond_it1.745
r_angle_refined_deg1.566
r_mcangle_it1.207
r_mcbond_it0.675
r_chiral_restr0.159
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.589
r_dihedral_angle_4_deg13.057
r_dihedral_angle_3_deg12.828
r_dihedral_angle_1_deg5.967
r_scangle_it2.722
r_scbond_it1.745
r_angle_refined_deg1.566
r_mcangle_it1.207
r_mcbond_it0.675
r_chiral_restr0.159
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms1432
Nucleic Acid Atoms
Solvent Atoms277
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing