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Priestia megaterium W130Q mutant of type 2 isoleucyl-tRNA synthetase complexed with an isoleucyl-adenylate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8C8V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 5 mM Ile-AMS and 16.5 mg/ml W130Q-PmIleRS2 were mixed in 1:1 ratio with the well solution containing: 0.2-0.5 M Potassium tartrate, 10-20 % (w/v) PEG3350, 25 mM Hepes-KOH pH=7,5 at 20 oC, 50 mM NaCl. The drop volume of 2 microliters, was equilibrated towards 300 microliters of the well solution at 4 degrees.
Crystal Properties Matthews coefficient Solvent content 2.99 58.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.22 α = 90 b = 108.22 β = 90 c = 240.44 γ = 90
Symmetry Space Group P 43 21 2
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 2M-F 2.9 T superbend magnet 2021-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9998692899475056 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 49.34 93.27 0.1511 0.1541 0.0301 0.999 22.62 25.6 64242 43.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 81 2.203 2.395 0.0301 0.531 1.38 21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 FREE R-VALUE 2.3 49.34 59947 3016 93.29 0.2031 0.201 0.2054 0.2411 0.2445 58.53
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 5.0364 f_angle_d 0.6132 f_chiral_restr 0.0427 f_plane_restr 0.0047 f_bond_d 0.0033
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8312 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building