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Crystal structure of ULK1 with a covalent compound GCL 99
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 277.15 20% w/v PEG 10000---- 0.1M Sodium HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.921 α = 90 b = 56.946 β = 90 c = 115.825 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 EIGER X 16M 2023-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00002 SLS X06SA
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 2.1 43.92 100 0.999 14.8 13.1 17644
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 2.1 2.16 0.804 2.7
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 2.1 41.1 16717 873 99.97 0.22305 0.22144 0.2299 0.25361 0.259 RANDOM 47.634
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] 0.1 0.69 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.191 r_dihedral_angle_4_deg 22.248 r_dihedral_angle_3_deg 17.3 r_long_range_B_other 11.214 r_long_range_B_refined 11.211 r_scangle_other 7.985 r_mcangle_it 6.354 r_mcangle_other 6.352 r_dihedral_angle_1_deg 5.949 r_scbond_it 5.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.191 r_dihedral_angle_4_deg 22.248 r_dihedral_angle_3_deg 17.3 r_long_range_B_other 11.214 r_long_range_B_refined 11.211 r_scangle_other 7.985 r_mcangle_it 6.354 r_mcangle_other 6.352 r_dihedral_angle_1_deg 5.949 r_scbond_it 5.434 r_scbond_other 5.431 r_mcbond_it 4.499 r_mcbond_other 4.496 r_angle_refined_deg 1.65 r_angle_other_deg 1.339 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 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 1901 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing