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Crystal structure of CLK3 in complex with macrocycle ODS2003136
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 20.0% PEG 3350, 0.20M NaI, 0.1M bis-tris propane pH 7.5, 10.0% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.05 59.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.168 α = 90 b = 116.909 β = 93.15 c = 71.161 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 2M 2012-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.12 19.87 97.2 0.147 0.175 0.093 6.3 3.4 55923
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.23 98.8 0.653 0.653 0.77 0.404 2 3.6
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 2eu9 2.12 19.58 53056 2839 97.13 0.1806 0.1779 0.1846 0.2301 0.233 RANDOM 22.885
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] -1.32 -0.02 0.35 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.392 r_sphericity_bonded 22.963 r_sphericity_free 22.881 r_dihedral_angle_4_deg 17.579 r_dihedral_angle_3_deg 14.628 r_dihedral_angle_1_deg 6.11 r_angle_refined_deg 1.564 r_angle_other_deg 0.932 r_chiral_restr 0.098 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.392 r_sphericity_bonded 22.963 r_sphericity_free 22.881 r_dihedral_angle_4_deg 17.579 r_dihedral_angle_3_deg 14.628 r_dihedral_angle_1_deg 6.11 r_angle_refined_deg 1.564 r_angle_other_deg 0.932 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5836 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms 130
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing