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Kinase domain of mutant human ULK1 in complex with compound MRT67307
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 3.6 65.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.6 α = 90 b = 152.6 β = 90 c = 206.14 γ = 120
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 1.836 111.255 99.5 1 20.2 18.4 79997
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 1.836 1.867 0.81 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.836 111.255 79997 4146 99.545 0.177 0.1756 0.1762 0.2113 0.212 32.223
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] -0.235 -0.118 -0.235 0.762
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.165 r_dihedral_angle_3_deg 15.956 r_lrange_it 9.195 r_lrange_other 9.119 r_dihedral_angle_2_deg 8.457 r_scangle_it 7.212 r_scangle_other 7.211 r_dihedral_angle_1_deg 6.069 r_mcangle_it 4.761 r_mcangle_other 4.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.165 r_dihedral_angle_3_deg 15.956 r_lrange_it 9.195 r_lrange_other 9.119 r_dihedral_angle_2_deg 8.457 r_scangle_it 7.212 r_scangle_other 7.211 r_dihedral_angle_1_deg 6.069 r_mcangle_it 4.761 r_mcangle_other 4.76 r_scbond_it 4.684 r_scbond_other 4.683 r_mcbond_it 3.449 r_mcbond_other 3.449 r_angle_refined_deg 1.663 r_angle_other_deg 0.554 r_xyhbond_nbd_refined 0.244 r_nbd_refined 0.222 r_symmetry_nbd_other 0.191 r_nbd_other 0.189 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.097 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.082 r_symmetry_nbd_refined 0.077 r_bond_refined_d 0.011 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 446 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing