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Kinase domain of mutant human ULK1 in complex with compound MRT68921
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 3.5 64.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.26 α = 90 b = 109.94 β = 93.775 c = 96.22 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 2023-05-05 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 2.209 85.075 99.7 0.999 16.6 6.6 88463
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 2.209 2.247 99.2 0.714 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 2.209 85.075 88461 4466 99.649 0.178 0.177 0.1776 0.2043 0.2048 40.344
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] 0.246 -1.165 -1.31 1.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.703 r_dihedral_angle_6_deg 16.695 r_dihedral_angle_2_deg 10.849 r_dihedral_angle_other_2_deg 10.202 r_lrange_it 9.143 r_lrange_other 9.136 r_scangle_it 7.675 r_scangle_other 7.671 r_dihedral_angle_1_deg 6.167 r_mcangle_it 5.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.703 r_dihedral_angle_6_deg 16.695 r_dihedral_angle_2_deg 10.849 r_dihedral_angle_other_2_deg 10.202 r_lrange_it 9.143 r_lrange_other 9.136 r_scangle_it 7.675 r_scangle_other 7.671 r_dihedral_angle_1_deg 6.167 r_mcangle_it 5.104 r_mcangle_other 5.103 r_scbond_it 4.977 r_scbond_other 4.957 r_mcbond_it 3.605 r_mcbond_other 3.604 r_angle_refined_deg 1.427 r_angle_other_deg 0.478 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.182 r_nbd_other 0.18 r_symmetry_xyhbond_nbd_refined 0.123 r_ncsr_local_group_6 0.1 r_ncsr_local_group_3 0.098 r_ncsr_local_group_4 0.096 r_ncsr_local_group_1 0.093 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_2 0.08 r_ncsr_local_group_5 0.075 r_chiral_restr 0.071 r_symmetry_xyhbond_nbd_other 0.027 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 8649 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling MOLREP phasing