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Crystal structure of CLK1 in complex with inhibitor 8g
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 20% PEG3350, 0.1 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.6 52.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.64 α = 90 b = 64.21 β = 127.67 c = 88.36 γ = 90
Symmetry Space Group C 1 2 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 2014-07-24 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) 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 1.45 23.65 99.1 0.044 9.9 3 71117 16.6
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 1.45 1.53 97.5 0.381 2.2 2.9
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 5J1W 1.45 23.65 67599 3494 98.87 0.16562 0.16411 0.1636 0.19533 0.195 RANDOM 26.987
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] 0.61 0.51 -0.71 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 18.678 r_dihedral_angle_3_deg 12.43 r_long_range_B_refined 7.601 r_long_range_B_other 7.6 r_dihedral_angle_1_deg 5.988 r_scangle_other 3.441 r_scbond_it 2.167 r_scbond_other 2.166 r_mcangle_it 1.999
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 18.678 r_dihedral_angle_3_deg 12.43 r_long_range_B_refined 7.601 r_long_range_B_other 7.6 r_dihedral_angle_1_deg 5.988 r_scangle_other 3.441 r_scbond_it 2.167 r_scbond_other 2.166 r_mcangle_it 1.999 r_mcangle_other 1.999 r_angle_refined_deg 1.675 r_mcbond_it 1.326 r_mcbond_other 1.325 r_angle_other_deg 0.851 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2760 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing