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Kinase domain of mutant human ULK1 in complex with compound XMD-17-51
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 3.51 64.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.47 α = 90 b = 109.54 β = 92.839 c = 96.52 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 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 1.829 96.402 100 0.999 20.5 6.6 156366
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 1.829 1.86 99.9 0.723 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 1.829 96.402 156364 7671 99.949 0.167 0.1657 0.1661 0.1891 0.1896 30.298
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] -0.199 -0.422 -0.3 0.538
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.411 r_dihedral_angle_2_deg 15.851 r_dihedral_angle_3_deg 15.771 r_lrange_it 8.915 r_lrange_other 8.813 r_scangle_it 7.201 r_scangle_other 7.201 r_dihedral_angle_1_deg 5.65 r_scbond_it 4.708 r_scbond_other 4.707
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.411 r_dihedral_angle_2_deg 15.851 r_dihedral_angle_3_deg 15.771 r_lrange_it 8.915 r_lrange_other 8.813 r_scangle_it 7.201 r_scangle_other 7.201 r_dihedral_angle_1_deg 5.65 r_scbond_it 4.708 r_scbond_other 4.707 r_mcangle_it 4.381 r_mcangle_other 4.381 r_mcbond_it 3.236 r_mcbond_other 3.227 r_angle_refined_deg 1.612 r_angle_other_deg 0.523 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.191 r_nbd_other 0.188 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.164 r_ncsr_local_group_2 0.107 r_symmetry_xyhbond_nbd_refined 0.106 r_ncsr_local_group_1 0.106 r_ncsr_local_group_6 0.098 r_ncsr_local_group_5 0.097 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_3 0.08 r_ncsr_local_group_4 0.075 r_chiral_restr_other 0.047 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8644 Nucleic Acid Atoms Solvent Atoms 959 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing