☰ Navigation Tabs
Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 PEG 8000, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 1.7 27.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.752 α = 90 b = 61.752 β = 90 c = 64.894 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH Osmic mirrors 2004-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.95 25 96.7 0.041 25.3 3.3 10459 10459
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) 1.95 2.02 87.2 0.314 2.25 2.7 928
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT 1.95 25 9957 9957 500 96.91 0.20865 0.20546 0.27224 0.2588 RANDOM 33.317
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] -0.91 -0.45 -0.91 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.178 r_dihedral_angle_4_deg 23.935 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_1_deg 7.088 r_scangle_it 3.162 r_scbond_it 1.911 r_angle_refined_deg 1.324 r_mcangle_it 1.201 r_mcbond_it 0.73 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.178 r_dihedral_angle_4_deg 23.935 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_1_deg 7.088 r_scangle_it 3.162 r_scbond_it 1.911 r_angle_refined_deg 1.324 r_mcangle_it 1.201 r_mcbond_it 0.73 r_nbtor_refined 0.3 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1140 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing