☰ Navigation Tabs
Crystal structure of DYRK1A complexed with KuFal319 (compound 11)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YLL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 31% PEG 400, 0.2 M lithium sulfate and 0.1 M tris, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 244.882 α = 90 b = 65.395 β = 115.18 c = 148.055 γ = 90
Symmetry Space Group C 1 2 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 PILATUS3 2M 2013-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.8 133.982 97.6 0.122 0.143 0.072 7.5 3.6 51386 51386
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 98.5 0.535 0.535 0.625 0.316 1.4 3.7
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 4YLL 2.8 133.98 48750 2622 97.24 0.2073 0.2054 0.2115 0.242 0.2482 RANDOM 48.579
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] 1.76 -2.17 1.17 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_1_deg 5.683 r_angle_refined_deg 1.433 r_angle_other_deg 0.969 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.528 r_dihedral_angle_4_deg 18.567 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_1_deg 5.683 r_angle_refined_deg 1.433 r_angle_other_deg 0.969 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11328 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing