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Non-phosphorylated human CLK1 in complex with an indole inhibitor to 1.65 Ang
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 273 24% PEG 3350, 200mM MgCl2, 100mM Bis-Tris (pH 6.5)
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.764 α = 90 b = 68.764 β = 90 c = 285.004 γ = 120
Symmetry Space Group P 65 2 2
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 PILATUS3 S 6M 2013-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.93 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 50 99.6 0.103 16 6.5 49449
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68
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 2VAG 1.65 47.55 44954 2413 95.95 0.13887 0.13549 0.1398 0.20316 0.2046 RANDOM 19.39
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] -0.07 -0.07 -0.07 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_sphericity_free 30.513 r_dihedral_angle_4_deg 15.745 r_sphericity_bonded 13.936 r_dihedral_angle_3_deg 12.708 r_scangle_other 5.958 r_dihedral_angle_1_deg 5.781 r_long_range_B_refined 5.663 r_long_range_B_other 5.545 r_scbond_it 5.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.214 r_sphericity_free 30.513 r_dihedral_angle_4_deg 15.745 r_sphericity_bonded 13.936 r_dihedral_angle_3_deg 12.708 r_scangle_other 5.958 r_dihedral_angle_1_deg 5.781 r_long_range_B_refined 5.663 r_long_range_B_other 5.545 r_scbond_it 5.513 r_scbond_other 5.512 r_rigid_bond_restr 5.416 r_mcangle_other 3.672 r_mcangle_it 3.67 r_mcbond_it 3.041 r_mcbond_other 3.038 r_angle_refined_deg 1.859 r_angle_other_deg 0.908 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2737 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing