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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AJG PDB ENTRY 2AJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M BIS-TRIS PH 5.5, 17% W/V PEG 10000, 0.2 M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.2 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.75 α = 90 b = 62.16 β = 90 c = 76.99 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 2010-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.47 38.7 99.4 0.06 17.2 4.3 35180 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.51 98.4 0.81 2.3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2AJG 1.47 38.69 35180 1857 99.38 0.18459 0.18339 0.1815 0.2064 0.2064 RANDOM 16.287
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] 0.69 0.27 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.589 r_dihedral_angle_4_deg 13.057 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 5.967 r_scangle_it 2.722 r_scbond_it 1.745 r_angle_refined_deg 1.566 r_mcangle_it 1.207 r_mcbond_it 0.675 r_chiral_restr 0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.589 r_dihedral_angle_4_deg 13.057 r_dihedral_angle_3_deg 12.828 r_dihedral_angle_1_deg 5.967 r_scangle_it 2.722 r_scbond_it 1.745 r_angle_refined_deg 1.566 r_mcangle_it 1.207 r_mcbond_it 0.675 r_chiral_restr 0.159 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 Atoms Number Protein Atoms 1432 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing