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Crystal structure of alanyl-tRNA synthetase in complex with 5''-O-(N-(L-alanyl)-sulfamyoxyl) adenine without oligomerization domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RIQ 1RIQ, 1V7O experimental model PDB 1V7O 1RIQ, 1V7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 293 PEG6000, MES, succinic acid, glucose, pH 5.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.874 α = 117.31 b = 89.205 β = 90.4 c = 94.905 γ = 107.36
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 315 mirrors 2007-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 3.1 50 96.7 0.085 11.1 2.7 34772 79.5
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) 3.1 3.21 96.8 0.483 2.8 2.5 3487
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 1RIQ, 1V7O 3.1 50 32290 1706 96.47 0.20309 0.19938 0.1921 0.27211 0.2662 RANDOM 76.462
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] -2.75 1.87 1.2 2.92 -0.58 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.343 r_dihedral_angle_3_deg 20.451 r_dihedral_angle_4_deg 15.847 r_dihedral_angle_1_deg 6.304 r_scangle_it 2.144 r_angle_refined_deg 1.409 r_scbond_it 1.202 r_mcangle_it 1.006 r_mcbond_it 0.529 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.343 r_dihedral_angle_3_deg 20.451 r_dihedral_angle_4_deg 15.847 r_dihedral_angle_1_deg 6.304 r_scangle_it 2.144 r_angle_refined_deg 1.409 r_scbond_it 1.202 r_mcangle_it 1.006 r_mcbond_it 0.529 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11993 Nucleic Acid Atoms Solvent Atoms 2 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing