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Crystal structure of human cytosolic aspartyl-tRNA synthetase, a component of multi-tRNA synthetase complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ASZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 20% PEG3350, 8% tacsimate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.2 43.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.885 α = 90 b = 141.921 β = 102.19 c = 68.495 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 CCD ADSC QUANTUM 315r 2013-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.24 50 99.3 48428 2.4 2.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 95.4
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 (All) 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 1ASZ 2.24 50 45979 2419 98.73 0.19876 0.19876 0.19724 0.1986 0.22775 0.2228 RANDOM 34.184
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] 1.36 -2.66 -1.86 -0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_dihedral_angle_3_deg 18.275 r_dihedral_angle_4_deg 18.174 r_dihedral_angle_1_deg 5.965 r_scangle_it 2.866 r_scbond_it 1.689 r_angle_refined_deg 1.29 r_mcangle_it 1.23 r_mcbond_it 0.644 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.42 r_dihedral_angle_3_deg 18.275 r_dihedral_angle_4_deg 18.174 r_dihedral_angle_1_deg 5.965 r_scangle_it 2.866 r_scbond_it 1.689 r_angle_refined_deg 1.29 r_mcangle_it 1.23 r_mcbond_it 0.644 r_chiral_restr 0.094 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6949 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 48
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling