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Crystal structure of human CLK3 in complex with RNAZ88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 20% PEG3350
0.1M bis-tris propane
0.2 Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.933 α = 93.81 b = 57.277 β = 103.74 c = 73.783 γ = 110.64
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 2024-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.95374 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 52.92 98.1 0.991 7.2 3.6 22505
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.688
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 2.5 52.92 21280 1090 98.15 0.22414 0.22158 0.2278 0.27228 0.2691 RANDOM 48
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] -2.7 1.26 1.24 0.27 0.03 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.202 r_dihedral_angle_2_deg 9.553 r_long_range_B_refined 8.601 r_long_range_B_other 8.6 r_dihedral_angle_1_deg 6.919 r_scangle_other 6.243 r_mcangle_it 6.1 r_mcangle_other 6.099 r_scbond_it 3.974 r_scbond_other 3.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.202 r_dihedral_angle_2_deg 9.553 r_long_range_B_refined 8.601 r_long_range_B_other 8.6 r_dihedral_angle_1_deg 6.919 r_scangle_other 6.243 r_mcangle_it 6.1 r_mcangle_other 6.099 r_scbond_it 3.974 r_scbond_other 3.973 r_mcbond_it 3.922 r_mcbond_other 3.915 r_angle_refined_deg 1.437 r_angle_other_deg 0.492 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 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 5401 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing PDB_EXTRACT data extraction