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Crystal structure of CLK1 in complex with compound 2 (CC513)
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 25% 1,2-propanediol, 10% glycerol, 0.1M sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.52 51.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.39 α = 90 b = 116.93 β = 99.04 c = 91.8 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 2014-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.93 31.01 99.9 0.114 0.125 0.051 0.997 8.2 5.6 88084
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) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.03 99.9 0.707 0.707 0.778 0.321 0.692 2.1 5.7
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 1.93 31.01 83367 4356 99.52 0.1764 0.1748 0.1842 0.2078 0.2157 RANDOM 41.413
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] -1.42 -0.72 1.52 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.117 r_dihedral_angle_4_deg 18.959 r_dihedral_angle_3_deg 13.414 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.57 r_angle_other_deg 1.159 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.117 r_dihedral_angle_4_deg 18.959 r_dihedral_angle_3_deg 13.414 r_dihedral_angle_1_deg 5.728 r_angle_refined_deg 1.57 r_angle_other_deg 1.159 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8280 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 142
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing