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Kinase domain of mutant human ULK1 in complex with compound CCT241533
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, HANGING DROP 6 277.15 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350
Crystal Properties Matthews coefficient Solvent content 3.46 64.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.65 α = 90 b = 96.31 β = 90 c = 109.19 γ = 90
Symmetry Space Group P 2 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 PILATUS 6M 2022-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.941 66.9 100 0.999 16.9 12.6 66660
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 1.941 1.974 100 0.682 2.2
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 1.941 66.9 66658 3377 99.97 0.171 0.1698 0.1701 0.193 0.1938 35.553
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] -0.564 0.148 0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.624 r_dihedral_angle_3_deg 15.557 r_lrange_it 8.914 r_lrange_other 8.874 r_scangle_it 7.73 r_scangle_other 7.729 r_dihedral_angle_2_deg 7.628 r_dihedral_angle_1_deg 5.907 r_scbond_it 5.138 r_scbond_other 5.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.624 r_dihedral_angle_3_deg 15.557 r_lrange_it 8.914 r_lrange_other 8.874 r_scangle_it 7.73 r_scangle_other 7.729 r_dihedral_angle_2_deg 7.628 r_dihedral_angle_1_deg 5.907 r_scbond_it 5.138 r_scbond_other 5.137 r_mcangle_other 4.472 r_mcangle_it 4.471 r_mcbond_other 3.534 r_mcbond_it 3.533 r_angle_refined_deg 1.596 r_angle_other_deg 0.527 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.185 r_nbd_other 0.163 r_symmetry_xyhbond_nbd_refined 0.124 r_ncsr_local_group_1 0.088 r_chiral_restr 0.083 r_symmetry_nbd_refined 0.083 r_symmetry_nbtor_other 0.081 r_chiral_restr_other 0.02 r_symmetry_xyhbond_nbd_other 0.017 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4296 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing