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Crystal structure of CLK1 in complex with macrocycle ODS2004070
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6G33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 17.5% isopropanol, 5% glycerol, 0.1M sodium/potassium phosphate
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.29 α = 90 b = 116.67 β = 98.59 c = 91.291 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 2014-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97623 Diamond I03
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 2.07 30.9 99.9 0.133 0.15 0.068 6.4 4.5 70856
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 2.07 2.18 99.9 0.721 0.721 0.817 0.376 2 4.4
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 6g33 2.07 30.9 67366 3463 99.86 0.1767 0.1749 0.2353 0.2128 0.2594 RANDOM 27.847
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] -1.37 -0.11 1.66 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.372 r_dihedral_angle_4_deg 16.895 r_dihedral_angle_3_deg 14.394 r_dihedral_angle_1_deg 5.712 r_angle_refined_deg 1.502 r_angle_other_deg 1.068 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.372 r_dihedral_angle_4_deg 16.895 r_dihedral_angle_3_deg 14.394 r_dihedral_angle_1_deg 5.712 r_angle_refined_deg 1.502 r_angle_other_deg 1.068 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8274 Nucleic Acid Atoms Solvent Atoms 418 Heterogen Atoms 107
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing