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Crystal structure of DYRK1A in complex with RD0392
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ANR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM Bis-Tris propane (pH 8.0), 200 mM Sodium fluoride and 18 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.63 α = 90 b = 88.182 β = 90 c = 228.038 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 DECTRIS PILATUS3 6M 2017-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.42 48.12 99.5 0.15 10.2 6.7 67838
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.48 1.432
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 3ANR 2.42 45 64462 3319 99.26 0.23414 0.23206 0.2321 0.27494 0.2749 RANDOM 52.568
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] -1.66 3.82 -2.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.321 r_dihedral_angle_4_deg 17.976 r_dihedral_angle_3_deg 13.371 r_long_range_B_refined 5.986 r_dihedral_angle_1_deg 4.565 r_mcangle_it 2.74 r_mcbond_it 1.533 r_scbond_it 1.405 r_angle_refined_deg 0.823 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.321 r_dihedral_angle_4_deg 17.976 r_dihedral_angle_3_deg 13.371 r_long_range_B_refined 5.986 r_dihedral_angle_1_deg 4.565 r_mcangle_it 2.74 r_mcbond_it 1.533 r_scbond_it 1.405 r_angle_refined_deg 0.823 r_chiral_restr 0.069 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11174 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 102
Software Software Software Name Purpose XDS data reduction MOLREP phasing Aimless data scaling REFMAC refinement