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The crystal structure of DYRK1a with a bound pyrido[2,3-d]pyrimidine inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX3 PDB entry 2VX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 15% PEG 300, 0.1M LiSO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.24 61.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 263.843 α = 90 b = 64.939 β = 115.16 c = 140.461 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 CCD RAYONIX MX225HE 2012-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-ID
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 2.35 50 99.4 0.09 8.9 3.8 90023 53
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 PDB entry 2VX3 2.35 39.83 85514 4498 99.7 0.20396 0.20178 0.2055 0.24582 0.2458 RANDOM 50.937
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] -0.12 -0.22 0.1 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.344 r_dihedral_angle_4_deg 19.083 r_dihedral_angle_3_deg 14.025 r_long_range_B_refined 7.567 r_long_range_B_other 7.55 r_dihedral_angle_1_deg 6.169 r_scangle_other 5.498 r_mcangle_it 5.239 r_mcangle_other 5.238 r_scbond_it 3.556
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.344 r_dihedral_angle_4_deg 19.083 r_dihedral_angle_3_deg 14.025 r_long_range_B_refined 7.567 r_long_range_B_other 7.55 r_dihedral_angle_1_deg 6.169 r_scangle_other 5.498 r_mcangle_it 5.239 r_mcangle_other 5.238 r_scbond_it 3.556 r_scbond_other 3.533 r_mcbond_it 3.449 r_mcbond_other 3.449 r_angle_refined_deg 1.511 r_angle_other_deg 0.892 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 10921 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 281
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling