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PylRS C-terminus domain mutant bound with L-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, 10% PEG 8000, 10% Ethylene Glycerol
Crystal Properties Matthews coefficient Solvent content 3.57 65.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.508 α = 90 b = 105.508 β = 90 c = 71.13 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 2.196 26.38 90.3 0.085 0.033 19.7 6.8 22987 30.0361379971
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 2.2 2.28 0.711 0.271 0.862
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 2.19639971537 26.377 1.33713986549 22458 1991 97.2165707112 0.196865263784 0.194483806635 0.1952 0.221309456342 0.2226 34.8688013953
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 22.116436551 f_angle_d 1.0728672336 f_chiral_restr 0.0643033540055 f_bond_d 0.00919169037347 f_plane_restr 0.006751880367
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2088 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing