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Crystal structure of CLK1 in complex with 5-iodotubercidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277.15 20% 1,2-propanediol, 5% glycerol and 0.1 M NaKPO4
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.181 α = 90 b = 116.191 β = 98.99 c = 90.98 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 2M 2014-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.0282 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 2.05 29.34 99.9 0.092 8.2 5.2 72225
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 2.05 2.16 99.9 0.627 2.1 5.1
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 2vag 2.05 89.86 68534 3576 99.75 0.18971 0.18824 0.1938 0.21829 0.2251 RANDOM 47.364
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] -0.26 0.33 -0.6 0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.281 r_sphericity_bonded 29.316 r_dihedral_angle_4_deg 19.167 r_dihedral_angle_3_deg 13.017 r_long_range_B_refined 6.325 r_long_range_B_other 6.325 r_dihedral_angle_1_deg 6.074 r_scangle_other 3.239 r_mcangle_it 2.57 r_mcangle_other 2.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.281 r_sphericity_bonded 29.316 r_dihedral_angle_4_deg 19.167 r_dihedral_angle_3_deg 13.017 r_long_range_B_refined 6.325 r_long_range_B_other 6.325 r_dihedral_angle_1_deg 6.074 r_scangle_other 3.239 r_mcangle_it 2.57 r_mcangle_other 2.57 r_scbond_it 1.974 r_scbond_other 1.971 r_mcbond_it 1.575 r_mcbond_other 1.575 r_angle_refined_deg 1.505 r_angle_other_deg 1.277 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8205 Nucleic Acid Atoms Solvent Atoms 341 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing