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Crystal structure of ULK1 in complex with inhibitor SBP-5147
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WNO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein concentration: 12.4 mg/ml.
Reservoir buffer: 3M ammonium sulfate, 0.1M citrate pH 5.0
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.185 α = 90 b = 74.185 β = 90 c = 220.73 γ = 90
Symmetry Space Group P 43 21 2
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 2018-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 19.82 99.9 0.107 0.998 11.4 7.2 42703
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 2.07 100 0.962 0.725 2.1 7.3
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 19.82 40428 2188 99.77 0.18519 0.18286 0.1933 0.22767 0.2307 RANDOM 37.34
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] 0.22 0.22 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_3_deg 13.995 r_long_range_B_other 6.475 r_long_range_B_refined 6.472 r_dihedral_angle_1_deg 6.21 r_scangle_other 4.272 r_mcangle_it 2.814 r_mcangle_other 2.814 r_scbond_it 2.749
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.166 r_dihedral_angle_4_deg 18.672 r_dihedral_angle_3_deg 13.995 r_long_range_B_other 6.475 r_long_range_B_refined 6.472 r_dihedral_angle_1_deg 6.21 r_scangle_other 4.272 r_mcangle_it 2.814 r_mcangle_other 2.814 r_scbond_it 2.749 r_scbond_other 2.748 r_mcbond_it 1.837 r_mcbond_other 1.837 r_angle_refined_deg 1.378 r_angle_other_deg 0.917 r_chiral_restr 0.072 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 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 4360 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing