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Structure of DYRK1A in complex with compound 58
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25% PEG 3350, 0.1M Hepes buffer pH 7.5, 0.2M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.4 48.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.25 α = 90 b = 84.95 β = 107.66 c = 84.91 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 2012-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.23 85 90.9 0.079 8.4 2.8 34961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.29 17.5 1.29 2.5
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 2vx3 2.3 25 32227 1714 96.57 0.2304 0.2275 0.2332 0.2837 0.288 RANDOM 34.217
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] 2.15 -1.09 -1.29 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_4_deg 22.721 r_dihedral_angle_3_deg 20.194 r_dihedral_angle_1_deg 5.634 r_angle_refined_deg 1.549 r_angle_other_deg 1.316 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_4_deg 22.721 r_dihedral_angle_3_deg 20.194 r_dihedral_angle_1_deg 5.634 r_angle_refined_deg 1.549 r_angle_other_deg 1.316 r_chiral_restr 0.086 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5418 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 59
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction