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Histone fold domain of AtNF-YB2/NF-YC3 in I2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 8 277 100 mM NaCl, 50 mM Tris-HCl pH 8.0 and 2 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.194 α = 90 b = 57.416 β = 99.364 c = 97.827 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2017-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.999996 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 49.4 99.6 0.018 1 13.9 6.7 11924 2.3 46.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 99.2 0.351 0.86 2.3 6.8
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 5G49 2.1 49.35 1.38 11898 577 99.25 0.1935 0.1928 0.1982 0.2073 0.2151 70.11
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 28.2565 f_angle_d 1.3451 f_chiral_restr 0.0703 f_bond_d 0.0142 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1389 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing