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Crystal structure of C. elegans XRN2 in complex with the XRN2-binding domain of PAXT-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other HOMOLOGY MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 6.5
Crystal Properties Matthews coefficient Solvent content 3.45 64.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.21 α = 90 b = 200.77 β = 90 c = 202.99 γ = 90
Symmetry Space Group P 21 21 21
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 6M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.84 50 94.6 0.13 7.1 3.2 155519 -3 72.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.91 84.5 1.26 0.75 3.1
Refinement Statistics Diffraction ID Structure Solution 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 HOMOLOGY MODEL 2.836 49.393 1.35 155484 3902 94.57 0.1867 0.1854 0.1959 0.2376 0.2439 86
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 14.663 f_angle_d 1.18 f_chiral_restr 0.063 f_bond_d 0.011 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33342 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 135
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing