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Crystal structure of CLK1 in complex with macrocycle ODS2003208
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 23% PEG3350, 0.1M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.88 57.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.173 α = 90 b = 69.173 β = 90 c = 330.581 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 6M 2014-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 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 1.6 30.65 99.9 0.075 0.077 0.018 21.2 16.9 63327
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 1.6 1.69 99.2 0.597 0.597 0.632 0.203 3.3 9.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6g33 1.6 30.65 60050 3126 99.8 0.1522 0.1508 0.1795 0.194 RANDOM 22.633
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] 0.38 0.19 0.38 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.489 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 11.557 r_dihedral_angle_1_deg 6.074 r_angle_refined_deg 1.656 r_angle_other_deg 0.839 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.489 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 11.557 r_dihedral_angle_1_deg 6.074 r_angle_refined_deg 1.656 r_angle_other_deg 0.839 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2735 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 120
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing