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NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabilized with C8-Hydrocarbon Linker
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4CSR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 277.15 0.1 M sodium cacodylate pH6.5
0.2 M calcium acetate
37% PEG600
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.01 α = 90 b = 52.21 β = 90 c = 72.99 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 PSI PILATUS 6M 2016-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.977930 SLS X10SA
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 2.5 50 99.6 0.997 11.07 12.2 6325
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 2.5 2.6 100 0.665 2.18 12.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4CSR 2.5 19.89 5661 635 99.67 0.1795 0.1724 0.1873 0.2412 0.1906 RANDOM 66.721
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] -0.46 0.37 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_3_deg 18.572 r_dihedral_angle_4_deg 15.199 r_dihedral_angle_1_deg 5.601 r_angle_refined_deg 1.627 r_angle_other_deg 1.145 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.79 r_dihedral_angle_3_deg 18.572 r_dihedral_angle_4_deg 15.199 r_dihedral_angle_1_deg 5.601 r_angle_refined_deg 1.627 r_angle_other_deg 1.145 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1526 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing PDB-REDO refinement