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Crystal Structure of NFIB Bound to TGGCA-Containing DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.04 M Potassium Phosphate monobasic, 16% (w/v) PEG 8000, and 20% (v/v) Glycerol
Crystal Properties Matthews coefficient Solvent content 2.35 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.873 α = 90 b = 54.183 β = 105.09 c = 58.721 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 100.15 PIXEL DECTRIS PILATUS3 6M 2024-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9785 SSRF BL18U1
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 2.3 50 98.7 0.2296 0.2509 0.0995 0.9825 11.3 6.36 11016
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 2.3 2.42 97.8 0.9162 0.999 0.3932 0.6406 6.27
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 9JH2 2.3 39.46 1.37 10990 1000 98.49 0.2219 0.2174 0.2174 0.2672 0.2672 41.49
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 24.4713 f_angle_d 0.5567 f_chiral_restr 0.038 f_plane_restr 0.0042 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1333 Nucleic Acid Atoms 486 Solvent Atoms 79 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Coot model building autoPX data processing PHASER phasing autoPX data reduction autoPX data scaling