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Crystal structure of H. pylori isoleucyl-tRNA synthetase (HpIleRS) in apo form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 0.1 M Hepes, pH 7.5, 2% (v/v) Tacsimate, and 20% (w/v) polyethylene glycol (PEG) 3,350
Crystal Properties Matthews coefficient Solvent content 2.59 52.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.623 α = 92.58 b = 52.776 β = 97.77 c = 103.254 γ = 103.71
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.9 48.31 97.09 0.0727 0.997 12.3 3.4 81231
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 90.2 1.53 0.663
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 48.31 77107 4124 97.08 0.15091 0.1508 0.1514 0.19096 0.191 RANDOM 22.946
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] 0.21 -0.01 -0.09 0.09 -0.19 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.87 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 14.1 r_long_range_B_refined 6.988 r_dihedral_angle_1_deg 5.773 r_scbond_it 3.529 r_mcangle_it 2.634 r_mcbond_it 1.907 r_angle_refined_deg 1.579 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.87 r_dihedral_angle_4_deg 16.24 r_dihedral_angle_3_deg 14.1 r_long_range_B_refined 6.988 r_dihedral_angle_1_deg 5.773 r_scbond_it 3.529 r_mcangle_it 2.634 r_mcbond_it 1.907 r_angle_refined_deg 1.579 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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_it r_scangle_other 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 7464 Nucleic Acid Atoms Solvent Atoms 1074 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing