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Structure of human NONO bound to (R)-SKBG-1 in p212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5 or Tris-HCl pH 8.5, 25 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.33 47.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.258 α = 90 b = 127.098 β = 90 c = 201.445 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 EIGER X 16M 2024-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9785 SOLEIL PROXIMA 1
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 2.45 48 99.55 0.01048 0.01159 0.0491 0.998 9.89 5.4 611051 51.62
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.49 97.3 1.166 1.34 0.431 1
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 2.5 19.99 1.34 56041 2802 99.87 0.2005 0.1977 0.2012 0.2533 0.2556
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 20.009 f_angle_d 0.978 f_chiral_restr 0.049 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12002 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing