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Crystal structure of human CLK1 in complex with 10Z-Hymenialdisine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JOW 1JOW.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 277 PEG 6K, Bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.8 31.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.277 α = 90 b = 64.434 β = 119.19 c = 80.112 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 CCD MARMOSAIC 225 mm CCD 2005-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9184 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 50 99.8 45196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1JOW.pdb 1.7 29.3 40775 40775 2173 95.01 0.14014 0.13765 0.1512 0.18581 0.1966 RANDOM 18.72
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] 0.48 0.46 -0.58 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 20.028 r_dihedral_angle_3_deg 11.532 r_sphericity_free 7.032 r_scangle_it 6.814 r_dihedral_angle_1_deg 5.85 r_scbond_it 5.216 r_mcangle_it 4.35 r_sphericity_bonded 3.696 r_mcbond_it 3.679
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.84 r_dihedral_angle_4_deg 20.028 r_dihedral_angle_3_deg 11.532 r_sphericity_free 7.032 r_scangle_it 6.814 r_dihedral_angle_1_deg 5.85 r_scbond_it 5.216 r_mcangle_it 4.35 r_sphericity_bonded 3.696 r_mcbond_it 3.679 r_rigid_bond_restr 2.634 r_mcbond_other 2.161 r_angle_refined_deg 1.591 r_angle_other_deg 0.845 r_symmetry_vdw_other 0.325 r_nbd_refined 0.221 r_nbd_other 0.179 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.095 r_nbtor_other 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2674 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing