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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H3N PDB ENTRY 1H3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN 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 coefficient Solvent content 3.5 64.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.83 α = 90 b = 154.23 β = 90 c = 174.95 γ = 90
Symmetry Space Group C 2 2 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 CCD 2006-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.85 50 99.3 0.06 13.86 4.1 472672
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 1.85 1.9 91.2 0.55 2.42 3.7
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 1H3N 1.85 87.37 112717 3477 99.5 0.181 0.18 0.1851 0.202 0.2054 RANDOM 21.12
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] -0.16 0.85 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.152 r_dihedral_angle_4_deg 19.74 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 6.04 r_scangle_it 3.369 r_scbond_it 2.341 r_angle_refined_deg 1.494 r_mcangle_it 1.375 r_mcbond_it 1.295 r_angle_other_deg 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.152 r_dihedral_angle_4_deg 19.74 r_dihedral_angle_3_deg 12.839 r_dihedral_angle_1_deg 6.04 r_scangle_it 3.369 r_scbond_it 2.341 r_angle_refined_deg 1.494 r_mcangle_it 1.375 r_mcbond_it 1.295 r_angle_other_deg 0.94 r_symmetry_vdw_other 0.34 r_nbd_refined 0.211 r_nbd_other 0.197 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.106 r_nbtor_other 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6608 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing