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PylRS C-terminus domain mutant bound with 3-Benzothienyl-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 3.8 67.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.252 α = 90 b = 105.252 β = 90 c = 71.701 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 MX300-HS 2017-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 0.99984 NSRRC TPS 05A
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 1.8958 38.463 99.77 0.068 0.02 36.4 11.3 35849 30.3947927499
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 1.9 1.97 0.735 0.226 2.5
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 1.8959014841 38.4629946681 1.3764791465 35848 1986 99.7523443804 0.181043746981 0.179803739962 0.1809 0.2018395396 0.2023 40.3724953184
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 22.2022030651 f_angle_d 1.04163316492 f_chiral_restr 0.0591905141891 f_bond_d 0.00891869226044 f_plane_restr 0.00574419093079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2090 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing