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PylRS C-terminus domain mutant bound with 3-(1-Naphthyl)-L-alanine 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, 10% PEG 8000, 10% Ethylene Glycerol
Crystal Properties Matthews coefficient Solvent content 3.85 68.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.723 α = 90 b = 105.723 β = 90 c = 71.597 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 1.0 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 2.5 28.201 98.96 0.094 0.029 38.1 10.6 15881 46.2538928928
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 0.513 0.171 3.4 8.4
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 2.50013285673 26.43075 1.34760112684 15881 1573 99.9874079204 0.178766103593 0.177338201625 0.1802 0.191717684171 0.1961 54.2116976936
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 27.0038157782 f_angle_d 1.21320832726 f_chiral_restr 0.0725725139975 f_bond_d 0.00942702228552 f_plane_restr 0.00858677695534
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2092 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing