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Crystal structure of ULK2 in complex with inhibitor SBP-5147
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QAV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein concentration: 12 mg/ml. Reservoir buffer: 30% PEG 3350, 0.1M sodium citrate pH 5.9, 0.15M MgCl2, 0.1M bis-tris pH 6.0.
Cryoprotectant: 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.19 43.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.55 α = 90 b = 78.08 β = 98.76 c = 94.22 γ = 90
Symmetry Space Group P 1 21 1
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 2M-F 2018-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
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 1.97 63.67 100 0.078 0.085 0.033 0.999 13.1 6.4 77687
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 1.97 2.04 0.919 1 0.393 0.669 6.3
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 1.97 63.67 73826 3842 100 0.19463 0.19281 0.1993 0.22975 0.2334 RANDOM 48.871
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] 0.12 0.51 -1.66 1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.38 r_dihedral_angle_4_deg 20.233 r_dihedral_angle_3_deg 13.613 r_long_range_B_refined 7.353 r_long_range_B_other 7.353 r_dihedral_angle_1_deg 6.482 r_scangle_other 3.55 r_mcangle_it 3.453 r_mcangle_other 3.453 r_scbond_it 2.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.38 r_dihedral_angle_4_deg 20.233 r_dihedral_angle_3_deg 13.613 r_long_range_B_refined 7.353 r_long_range_B_other 7.353 r_dihedral_angle_1_deg 6.482 r_scangle_other 3.55 r_mcangle_it 3.453 r_mcangle_other 3.453 r_scbond_it 2.255 r_scbond_other 2.255 r_mcbond_it 2.05 r_mcbond_other 2.05 r_angle_refined_deg 1.345 r_angle_other_deg 0.946 r_chiral_restr 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 8339 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 201
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing