☰ Navigation Tabs
Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix (selenomethionine derivative)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 293 1.5M ammonium sulfate in 0.1M HEPES (pH7.5) buffer, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82 α = 90 b = 103.7 β = 90 c = 112.7 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 QUANTUM 4 2006-11-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00, 0.97898, 0.97966 Photon Factory BL-17A
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 2.5 50 100 0.08 46.5 14.5 17033
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 2.5 2.59 100 0.268 14.2 14.7 1665
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MAD THROUGHOUT 2.5 41 16983 16983 859 100 0.17 0.17 0.141 0.24 0.2091 RANDOM 22
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] 0.01 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.672 r_dihedral_angle_4_deg 16.345 r_dihedral_angle_3_deg 16.161 r_dihedral_angle_1_deg 14.622 r_scangle_it 5.341 r_scbond_it 3.442 r_angle_refined_deg 1.956 r_mcangle_it 1.909 r_mcbond_it 1.315 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.672 r_dihedral_angle_4_deg 16.345 r_dihedral_angle_3_deg 16.161 r_dihedral_angle_1_deg 14.622 r_scangle_it 5.341 r_scbond_it 3.442 r_angle_refined_deg 1.956 r_mcangle_it 1.909 r_mcbond_it 1.315 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.205 r_symmetry_hbond_refined 0.166 r_chiral_restr 0.129 r_metal_ion_refined 0.039 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 3710 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing