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14-3-3 sigma with RelA/p65 binding site pS45 and covalently bound TCF521
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.095 M HEPES Na pH 7.1, 27% PEG400, 0.19M Calcium chloride, 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.48 50.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.542 α = 90 b = 112.151 β = 90 c = 62.61 γ = 90
Symmetry Space Group C 2 2 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 DECTRIS PILATUS 6M-F 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03320 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.23 62.61 100 0.069 0.073 0.997 14.3 8.6 84336
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.23 1.26 100 0.513 0.557 0.855 2.9
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 FREE R-VALUE 3MHR 1.23 45.62 79959 4352 99.98 0.17624 0.17512 0.1845 0.19737 0.2041 RANDOM 15.966
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] 0.54 -0.23 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.162 r_dihedral_angle_4_deg 14.792 r_dihedral_angle_3_deg 12.032 r_long_range_B_refined 5.325 r_long_range_B_other 4.934 r_dihedral_angle_1_deg 4.85 r_scangle_other 3.812 r_scbond_it 2.637 r_scbond_other 2.635 r_mcangle_other 2.577
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.162 r_dihedral_angle_4_deg 14.792 r_dihedral_angle_3_deg 12.032 r_long_range_B_refined 5.325 r_long_range_B_other 4.934 r_dihedral_angle_1_deg 4.85 r_scangle_other 3.812 r_scbond_it 2.637 r_scbond_other 2.635 r_mcangle_other 2.577 r_mcangle_it 2.575 r_angle_refined_deg 1.946 r_mcbond_it 1.612 r_mcbond_other 1.604 r_angle_other_deg 1.208 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1869 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing