☰ Navigation Tabs
PylRS C-terminus domain mutant bound with D-3-trifluoromethylphenylalanine and AMPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZCE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 100 mM HEPES buffer at pH 7.5, 10% PEG 8000, 10% Ethylene Glycerol
Crystal Properties Matthews coefficient Solvent content 3.79 67.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.67 α = 90 b = 104.67 β = 90 c = 71.813 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RAYONIX MX300HE 2017-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 1.899801 35 98.9 0.092 0.034 21.4 6.9 34993 19.8583536783
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 0.97 0.371 0.745
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 FREE R-VALUE 2ZCE 1.89980982122 34.2612998565 1.36297285096 33834 1999 95.6330026287 0.185072516224 0.183677326204 0.1842 0.207290389712 0.2083 24.9292408815
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 23.608636724 f_angle_d 1.02826894311 f_chiral_restr 0.0761210379842 f_bond_d 0.0083356132286 f_plane_restr 0.00618201342641
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2106 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing