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NONO homodimer bound to (R)-SKBG-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IFM A/B dimer search
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1 M Sodium HEPES pH 8
26% (w/v) PEG 2000 MME
1:1 drop:reservoir
cryprotected with 20% glycerol
Crystal Properties Matthews coefficient Solvent content 2.62 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.627 α = 90 b = 71.141 β = 118.656 c = 101.748 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2023-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.52 48.31 99.3 0.045 0.062 0.033 0.998 11.6 3.5 40730 75.15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.63 97.6 1.046 1.232 0.646 0.475 1.2 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.52 48.31 1.34 40721 2129 99.29 0.2274 0.225 0.2256 0.2681 0.2688 93.5
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 14.3028 f_angle_d 0.3987 f_chiral_restr 0.0383 f_plane_restr 0.0035 f_bond_d 0.0016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7983 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 112
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing