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NF-YB/C Heterodimer in Complex with NF-YA Peptide
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 Tris pH9.0
0.2 M NaAc
30% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.9 α = 90 b = 52.9 β = 90 c = 134.1 γ = 120
Symmetry Space Group P 32 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 100 PIXEL PSI PILATUS 6M 2016-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.978570 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 50 99.8 0.999 21.85 18.9 15380
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 2.1 100 0.846 2.81 18.9
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 18.92 14573 766 99.82 0.2005 0.1984 0.2105 0.2406 0.2609 RANDOM 67.801
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] 0.43 0.21 0.43 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.089 r_dihedral_angle_3_deg 14.757 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_1_deg 5.205 r_angle_refined_deg 1.372 r_angle_other_deg 1.124 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.089 r_dihedral_angle_3_deg 14.757 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_1_deg 5.205 r_angle_refined_deg 1.372 r_angle_other_deg 1.124 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1581 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing