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Crystal structure of Human CSNK1A1 with A86
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FQD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277.15 CSNK1A1 at a concentration of 5.8 mg/ml (50 mM Tris-HCl, 300 mM NaCl, 0.25 mM TCEP, pH 8.0) was pre-incubated with 0.7 mM (4.7-fold molar excess) of Mg2+-ATP (120 mM in UPW) for 1 h. 0.1 uL of the protein solution was then mixed with 0.1 uL of reservoir solution (0.10 M MES/NaOH pH 6.8, 10.0% 2-propanol, 26.0% PEG400) and equilibrated at 4 C over 0.06mL of reservoir solution. Well diffracting crystals appeared within 4 days and grew to full size over 23 days.
Crystal Properties Matthews coefficient Solvent content 3.02 59.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.383 α = 90 b = 113.383 β = 90 c = 80.878 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100.5 PIXEL DECTRIS PILATUS3 2M 2017-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.28 29.31 98.1 0.07 13.3 4 22991
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.4 0.56
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 5FQD 2.28 29.31 21917 1071 98.01 0.17709 0.17496 0.1843 0.22117 0.2282 RANDOM 58.303
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] -0.21 -0.21 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.433 r_dihedral_angle_3_deg 13.346 r_dihedral_angle_4_deg 11.595 r_long_range_B_refined 9.954 r_long_range_B_other 9.949 r_scangle_other 7.515 r_mcangle_it 6.226 r_mcangle_other 6.224 r_dihedral_angle_1_deg 5.586 r_scbond_it 5.056
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.433 r_dihedral_angle_3_deg 13.346 r_dihedral_angle_4_deg 11.595 r_long_range_B_refined 9.954 r_long_range_B_other 9.949 r_scangle_other 7.515 r_mcangle_it 6.226 r_mcangle_other 6.224 r_dihedral_angle_1_deg 5.586 r_scbond_it 5.056 r_scbond_other 5.055 r_mcbond_it 4.327 r_mcbond_other 4.325 r_angle_other_deg 3.585 r_angle_refined_deg 1.182 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_other 0.006 r_gen_planes_refined 0.004 r_bond_other_d 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 2456 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 141
Software Software Software Name Purpose REFMAC refinement SCALA data scaling REFMAC phasing MOSFLM data reduction