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DYRK1A complex with DYR530
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 1.8 M sodium malonate, 1.3% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.27 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.472 α = 90 b = 83.213 β = 90 c = 146.675 γ = 90
Symmetry Space Group P 21 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 Bruker PHOTON III 2023-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34
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 1.85 24.88 100 0.119 0.996 10.7 7 67138
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 1.85 1.89 100 0.76 0.48 2 4.6
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 (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 1.85 24.88 63675 3381 99.92 0.16584 0.16329 0.1983 0.21303 0.2225 RANDOM 21.451
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] -0.28 0.11 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.02 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_1_deg 6.871 r_long_range_B_refined 3.853 r_long_range_B_other 3.75 r_rigid_bond_restr 3.099 r_scangle_other 2.286 r_mcangle_it 2.217 r_mcangle_other 2.217 r_scbond_it 1.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.02 r_dihedral_angle_3_deg 15.441 r_dihedral_angle_1_deg 6.871 r_long_range_B_refined 3.853 r_long_range_B_other 3.75 r_rigid_bond_restr 3.099 r_scangle_other 2.286 r_mcangle_it 2.217 r_mcangle_other 2.217 r_scbond_it 1.548 r_scbond_other 1.548 r_angle_refined_deg 1.498 r_mcbond_it 1.439 r_mcbond_other 1.439 r_angle_other_deg 0.499 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5581 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 93
Software Software Software Name Purpose REFMAC refinement PROTEUM2 data reduction Aimless data scaling MOLREP phasing