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NF-Kappa-B1 Bound with a Covalent Inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 0.1 M Citrate pH5.0, 20%w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.21 α = 90 b = 57.21 β = 90 c = 71.85 γ = 120
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 2023-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00000 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.02 49.55 100 0.075 0.079 0.024 0.999 17.1 10.5 17269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.07 100 1.06 1.116 0.346 0.679 10.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.02 49.55 16462 802 99.97 0.1837 0.18164 0.1725 0.22665 0.2133 RANDOM 49.667
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] 0.53 0.53 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.16 r_dihedral_angle_1_deg 7.447 r_long_range_B_refined 7.192 r_long_range_B_other 7.175 r_scangle_other 4.508 r_mcangle_it 3.926 r_mcangle_other 3.925 r_dihedral_angle_2_deg 3.799 r_scbond_it 2.684 r_scbond_other 2.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.16 r_dihedral_angle_1_deg 7.447 r_long_range_B_refined 7.192 r_long_range_B_other 7.175 r_scangle_other 4.508 r_mcangle_it 3.926 r_mcangle_other 3.925 r_dihedral_angle_2_deg 3.799 r_scbond_it 2.684 r_scbond_other 2.683 r_mcbond_it 2.578 r_mcbond_other 2.578 r_angle_refined_deg 1.165 r_angle_other_deg 0.413 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1557 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing