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Crystal structure of human CLK3 in complex with AZ176
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9EZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 25% PEG 3350
0,2M NaI
10% Ethylene Glycol
0.1M bis-tris propane 6.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.777 α = 90 b = 45.425 β = 115.08 c = 83.839 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 EIGER2 XE 16M 2025-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 39.28 100 0.127 0.141 0.059 0.996 8.4 5.5 22158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 0.796 0.88 0.37 0.76 5.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 39.25 21070 1081 99.95 0.20342 0.20124 0.2137 0.24635 0.2519 RANDOM 34.291
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] -0.24 1.38 -2.08 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.459 r_dihedral_angle_2_deg 5.918 r_dihedral_angle_1_deg 5.799 r_long_range_B_refined 5.216 r_long_range_B_other 5.215 r_scangle_other 3.682 r_mcangle_other 3.024 r_mcangle_it 3.02 r_scbond_it 2.309 r_scbond_other 2.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.459 r_dihedral_angle_2_deg 5.918 r_dihedral_angle_1_deg 5.799 r_long_range_B_refined 5.216 r_long_range_B_other 5.215 r_scangle_other 3.682 r_mcangle_other 3.024 r_mcangle_it 3.02 r_scbond_it 2.309 r_scbond_other 2.308 r_mcbond_it 1.935 r_mcbond_other 1.92 r_angle_refined_deg 1.147 r_angle_other_deg 0.41 r_chiral_restr 0.052 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2800 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction