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Crystal structure of human CLK1 in complex with pyrido[3,4-g]quinazoline derivative ZW29 (compound 13)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 30% 1,2-propanediol, 10% glycerol and 50 mM Na/K phosphate pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.471 α = 90 b = 116.021 β = 99.28 c = 90.108 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 PILATUS3 6M 2014-08-18 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) 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 2.52 35.47 99.8 0.119 7.6 4.8 38700 51.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.66 99.8 0.829 2 4.5
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 1Z57 2.52 35.47 36746 1897 99.73 0.20134 0.1991 0.2059 0.24366 0.247 RANDOM 71.461
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] -2.59 0.32 3.76 -1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.843 r_dihedral_angle_4_deg 23.127 r_dihedral_angle_3_deg 13.879 r_long_range_B_other 6.974 r_long_range_B_refined 6.973 r_dihedral_angle_1_deg 6 r_scangle_other 4.992 r_mcangle_it 4.109 r_mcangle_other 4.107 r_scbond_it 3.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.843 r_dihedral_angle_4_deg 23.127 r_dihedral_angle_3_deg 13.879 r_long_range_B_other 6.974 r_long_range_B_refined 6.973 r_dihedral_angle_1_deg 6 r_scangle_other 4.992 r_mcangle_it 4.109 r_mcangle_other 4.107 r_scbond_it 3.186 r_scbond_other 3.185 r_mcbond_it 2.638 r_mcbond_other 2.637 r_angle_refined_deg 1.217 r_angle_other_deg 0.848 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 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 7927 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing