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Crystal structure of ULK2 in complexed with hesperadin
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, SITTING DROP 293.15 27.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.75, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.16 43.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.208 α = 90 b = 77.561 β = 97.77 c = 94.941 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 EIGER X 16M 2018-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.77 48.75 99.2 0.071 0.997 10.1 5.1 27487 82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.92 99.3 0.758 0.884 2 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4WNO 2.77 48.75 26116 1357 99.05 0.21993 0.21776 0.2197 0.2616 0.2618 RANDOM 108.746
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] 3.07 -1.81 0.82 -3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.954 r_dihedral_angle_4_deg 19.171 r_dihedral_angle_3_deg 15.867 r_dihedral_angle_1_deg 7.812 r_long_range_B_refined 7.189 r_long_range_B_other 7.189 r_scangle_other 4.997 r_mcangle_it 4.761 r_mcangle_other 4.761 r_scbond_it 3.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.954 r_dihedral_angle_4_deg 19.171 r_dihedral_angle_3_deg 15.867 r_dihedral_angle_1_deg 7.812 r_long_range_B_refined 7.189 r_long_range_B_other 7.189 r_scangle_other 4.997 r_mcangle_it 4.761 r_mcangle_other 4.761 r_scbond_it 3.081 r_scbond_other 3.081 r_mcbond_it 2.987 r_mcbond_other 2.987 r_angle_refined_deg 1.098 r_angle_other_deg 1.033 r_chiral_restr 0.038 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8141 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing