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The Crystal Structure of NF-kB-inducing Kinase (NIK) from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DN5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M MMT pH9.0, 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.652 α = 90 b = 119.652 β = 90 c = 115.586 γ = 90
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 PILATUS3 S 6M 2023-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18079 CLSI 08B1-1
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 2.9 48.56 100 0.992 11.2 9.4 36217
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 2.9 3.03 0.709
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 48.56 36186 1628 99.967 0.196 0.194 0.1951 0.2412 0.2417 49.624
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] 0.255 0.255 -0.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.249 r_dihedral_angle_6_deg 12.801 r_lrange_it 7.652 r_lrange_other 7.65 r_dihedral_angle_1_deg 6.144 r_dihedral_angle_2_deg 5.004 r_scangle_it 4.861 r_scangle_other 4.86 r_mcangle_other 4.829 r_mcangle_it 4.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.249 r_dihedral_angle_6_deg 12.801 r_lrange_it 7.652 r_lrange_other 7.65 r_dihedral_angle_1_deg 6.144 r_dihedral_angle_2_deg 5.004 r_scangle_it 4.861 r_scangle_other 4.86 r_mcangle_other 4.829 r_mcangle_it 4.828 r_mcbond_it 2.891 r_mcbond_other 2.878 r_scbond_it 2.877 r_scbond_other 2.877 r_angle_refined_deg 1.179 r_angle_other_deg 0.398 r_dihedral_angle_other_2_deg 0.319 r_nbd_refined 0.216 r_nbd_other 0.199 r_symmetry_nbd_other 0.185 r_symmetry_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.153 r_xyhbond_nbd_refined 0.126 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_2 0.066 r_symmetry_xyhbond_nbd_other 0.065 r_ncsr_local_group_4 0.063 r_ncsr_local_group_6 0.062 r_ncsr_local_group_3 0.061 r_ncsr_local_group_1 0.06 r_ncsr_local_group_5 0.059 r_chiral_restr 0.057 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10356 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing