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NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabilized with C11-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 0.1 M Tris pH8.5
0.2 M MgCl2
18% PEG8000
Crystal Properties Matthews coefficient Solvent content 1.84 33.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.95 α = 90 b = 49.76 β = 90 c = 74.5 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 2016-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.977970 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 1.8 19.06 99.4 0.999 20.16 12.4 17408
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 1.8 1.9 99 0.895 2.15 12.8
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 1.8 19.06 16497 868 99.44 0.2089 0.2078 0.219 0.2299 0.245 RANDOM 48.716
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] 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.35 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_4_deg 11.96 r_dihedral_angle_1_deg 4.874 r_angle_refined_deg 1.251 r_angle_other_deg 1.066 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.35 r_dihedral_angle_3_deg 13.775 r_dihedral_angle_4_deg 11.96 r_dihedral_angle_1_deg 4.874 r_angle_refined_deg 1.251 r_angle_other_deg 1.066 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1478 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing