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DYRK1A in complex with HG-8-60-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NCT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M KSCN; 0.05M KCl; 10% PEG 3350, pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.24 α = 90 b = 88.04 β = 90 c = 228.5 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 PILATUS 6M-F 2016-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.984003 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.45 50 99.2 0.107 0.997 14.24 6.4 66317
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.6 95.7 0.688 0.837 2.47 10626
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 4nct 2.42 48.4 63007 3302 95.8 0.21485 0.21341 0.2141 0.24192 0.2438 RANDOM 50.255
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] 16.81 5.48 -22.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.994 r_dihedral_angle_4_deg 16.714 r_dihedral_angle_3_deg 13.877 r_dihedral_angle_1_deg 5.71 r_long_range_B_refined 3.294 r_long_range_B_other 3.205 r_mcangle_it 1.471 r_mcangle_other 1.471 r_angle_refined_deg 1.237 r_scangle_other 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.994 r_dihedral_angle_4_deg 16.714 r_dihedral_angle_3_deg 13.877 r_dihedral_angle_1_deg 5.71 r_long_range_B_refined 3.294 r_long_range_B_other 3.205 r_mcangle_it 1.471 r_mcangle_other 1.471 r_angle_refined_deg 1.237 r_scangle_other 1.19 r_angle_other_deg 0.977 r_mcbond_it 0.835 r_mcbond_other 0.835 r_scbond_it 0.677 r_scbond_other 0.677 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_bond_other_d 0.004 r_gen_planes_refined 0.004 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 11006 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing