☰ Navigation Tabs
Crystal structure of murine NF-kappaB inducing kinase (NIK) in complex with compound 2f
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4G3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 277 0.3-0.9M ammonium sulphate,
0.05-0.1M sodium citrate,
0.7-1.0M Lithium sulphate
Crystal Properties Matthews coefficient Solvent content 3.17 61.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.83 α = 90 b = 144.83 β = 90 c = 46.53 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 PILATUS 6M-F 2013-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.84 36.21 98.1 0.104 0.981 11.7 6.1 21715
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.91 99.9 0.745 0.84 6.1
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 4G3E 2.84 36.21 21715 1171 98 0.237 0.234 0.2357 0.283 0.2815 RANDOM 76.77
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_3_deg 15.319 r_dihedral_angle_4_deg 14.664 r_long_range_B_refined 6.092 r_long_range_B_other 6.092 r_dihedral_angle_1_deg 5.477 r_mcangle_other 3.738 r_mcangle_it 3.737 r_scangle_other 3.631 r_mcbond_it 2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_3_deg 15.319 r_dihedral_angle_4_deg 14.664 r_long_range_B_refined 6.092 r_long_range_B_other 6.092 r_dihedral_angle_1_deg 5.477 r_mcangle_other 3.738 r_mcangle_it 3.737 r_scangle_other 3.631 r_mcbond_it 2.17 r_mcbond_other 2.166 r_scbond_it 2.111 r_scbond_other 2.111 r_angle_refined_deg 1.052 r_angle_other_deg 0.701 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 5020 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing