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Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A31 PDB ENTRY 3A31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.5M ammonium sulfate in 0.1M HEPES (pH7.5) buffer, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.23 44.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.486 α = 90 b = 103.71 β = 90 c = 112.537 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 2006-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.00 Photon Factory BL-6A
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 2.3 50 100 0.096 19.9 7.2 21565
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 2.3 2.38 99.9 0.3 6.9 7 2118
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3A31 2.3 38.3 21535 21154 1082 99.9 0.18 0.18 0.1512 0.24 0.218 RANDOM 14.341
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.705 r_dihedral_angle_3_deg 15.697 r_dihedral_angle_4_deg 15.512 r_dihedral_angle_1_deg 14.988 r_scangle_it 4.508 r_scbond_it 2.89 r_angle_refined_deg 1.913 r_mcangle_it 1.733 r_mcbond_it 1.082 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.705 r_dihedral_angle_3_deg 15.697 r_dihedral_angle_4_deg 15.512 r_dihedral_angle_1_deg 14.988 r_scangle_it 4.508 r_scbond_it 2.89 r_angle_refined_deg 1.913 r_mcangle_it 1.733 r_mcbond_it 1.082 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.201 r_chiral_restr 0.176 r_xyhbond_nbd_refined 0.167 r_metal_ion_refined 0.058 r_bond_refined_d 0.02 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 3706 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing