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NCS-1 bound to XChem ligand 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QI4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1 M sodium cacodylate trihydrate pH 6.5, 0.2 M sodium acetate trihydrate, 30% (v/v) polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.7 54.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.043 α = 90 b = 55.799 β = 95.192 c = 78.744 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 EIGER2 X 9M 2024-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.921 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.844 78.421 91.7 0.995 7 6.9 19589 20.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.844 2.145 0.67 1.7
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 1.9 46.38 1.34 19538 908 52.8 0.2361 0.2339 0.234 0.2816 0.2815 23.34
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 20.9948 f_angle_d 0.9917 f_chiral_restr 0.0508 f_bond_d 0.0126 f_plane_restr 0.0124
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2988 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 122
Software Software Software Name Purpose PHENIX refinement autoPROC data processing Coot model building PHASER phasing