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Structure of TNIK with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.889 α = 90 b = 89.595 β = 90 c = 97.577 γ = 90
Symmetry Space Group P 21 21 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 EIGER2 R 4M 2024-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97918 SSRF BL02U1
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 2.489 65.995 99.9 0.999 17.2 9.2 25206
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 2.489 2.59 0.777
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 2.489 65.995 25156 1315 99.885 0.259 0.2556 0.257 0.3263 0.3232 64.798
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] 1.798 2.347 -4.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.605 r_dihedral_angle_3_deg 14.16 r_dihedral_angle_4_deg 13.236 r_dihedral_angle_1_deg 5.3 r_lrange_it 4.509 r_lrange_other 4.485 r_mcangle_it 2.331 r_mcangle_other 2.331 r_scangle_it 1.439 r_scangle_other 1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.605 r_dihedral_angle_3_deg 14.16 r_dihedral_angle_4_deg 13.236 r_dihedral_angle_1_deg 5.3 r_lrange_it 4.509 r_lrange_other 4.485 r_mcangle_it 2.331 r_mcangle_other 2.331 r_scangle_it 1.439 r_scangle_other 1.439 r_mcbond_other 1.259 r_mcbond_it 1.258 r_angle_refined_deg 1.177 r_angle_other_deg 0.985 r_scbond_it 0.726 r_scbond_other 0.726 r_nbd_refined 0.155 r_symmetry_nbd_refined 0.155 r_symmetry_nbd_other 0.15 r_nbtor_refined 0.143 r_xyhbond_nbd_refined 0.124 r_nbd_other 0.117 r_symmetry_xyhbond_nbd_refined 0.111 r_symmetry_xyhbond_nbd_other 0.088 r_symmetry_nbtor_other 0.071 r_chiral_restr 0.033 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4843 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing