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Kinase domain of mutant human ULK1 in complex with compound WZ4003
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 3.42 64.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.09 α = 90 b = 96.09 β = 90 c = 108.9 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 2022-09-30 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 2.164 63.281 99.9 0.999 19.4 12.6 47753
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 2.164 2.201 100 0.697 2.1
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 2.164 63.281 47753 2331 99.937 0.169 0.1676 0.1675 0.2001 0.2003 46.156
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] 0.393 -0.029 -0.364
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.799 r_dihedral_angle_3_deg 15.83 r_dihedral_angle_2_deg 11.021 r_lrange_it 9.763 r_lrange_other 9.76 r_scangle_it 8.439 r_scangle_other 8.438 r_dihedral_angle_1_deg 6.267 r_scbond_it 5.668 r_scbond_other 5.668
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.799 r_dihedral_angle_3_deg 15.83 r_dihedral_angle_2_deg 11.021 r_lrange_it 9.763 r_lrange_other 9.76 r_scangle_it 8.439 r_scangle_other 8.438 r_dihedral_angle_1_deg 6.267 r_scbond_it 5.668 r_scbond_other 5.668 r_mcangle_it 5.295 r_mcangle_other 5.294 r_mcbond_it 3.997 r_mcbond_other 3.987 r_angle_refined_deg 1.525 r_angle_other_deg 0.502 r_nbd_refined 0.221 r_symmetry_nbd_other 0.189 r_xyhbond_nbd_refined 0.186 r_nbd_other 0.186 r_nbtor_refined 0.184 r_symmetry_nbd_refined 0.12 r_ncsr_local_group_1 0.096 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.077 r_symmetry_xyhbond_nbd_other 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4297 Nucleic Acid Atoms Solvent Atoms 272 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing