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Human mitochondrial aspartyl-tRNA synthetase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C0A HOMOLOGY MODEL BASED ON PDB ENTRY 1C0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 SITTING DROPLETS WERE PREPARED BY MIXING 0.5 UL HSADRS2 AT 10.6 MG/ML (IN 50 MM HEPES-NA PH 7.5, 150 MM NACL, 0.1 MM EDTA, 10% (V/V) GLYCEROL AND 1 MM DTT) WITH 0.5 UL BOTTOM PHASE OF A BIPHASIC MIXTURE OF 50 MM BIS-TRIS PH 5.5, 20% (M/V) PEG-3350 AND 1 M AMMONIUM SULFATE AND EQUILIBRATED BY VAPOR DIFFUSION OVER 50 UL OF THE LATTER SOLUTION.
Crystal Properties Matthews coefficient Solvent content 3.25 62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.4 α = 90 b = 82.6 β = 100.4 c = 146.3 γ = 90
Symmetry Space Group P 1 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 PIXEL DECTRIS PILATUS 6M 2010-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 3.7 89 98.8 0.18 9.4 7.2 35768 -3 88.02
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 3.7 3.8 91.2 0.64 2.1 4
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT HOMOLOGY MODEL BASED ON PDB ENTRY 1C0A 3.7 29.916 2 35680 1780 98.82 0.2222 0.2191 0.2217 0.2801 0.2808 108.2
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.145 f_angle_d 1.084 f_chiral_restr 0.08 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18840 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing