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Crystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RU7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 277.15 20% PEG 3350, 0.1 M sodium sulfate, and 0.1 M citrate, pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.061 α = 90.27 b = 81.813 β = 105.95 c = 89.088 γ = 93.6
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 EIGER2 X 16M 2020-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.96 47.09 93 0.048 0.067 0.034 0.998 12.2 3.8 88717
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.03 91.7 0.413 0.597 0.304 0.929 2 3.8
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 6RU7 1.96 47.09 84176 4541 92.99 0.1896 0.1879 0.2001 0.221 0.2304 RANDOM 42.477
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] -0.51 0.68 -0.53 3.37 0.39 -2.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.889 r_dihedral_angle_4_deg 16.689 r_dihedral_angle_3_deg 14.262 r_dihedral_angle_1_deg 6.82 r_angle_refined_deg 1.412 r_angle_other_deg 1.311 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.889 r_dihedral_angle_4_deg 16.689 r_dihedral_angle_3_deg 14.262 r_dihedral_angle_1_deg 6.82 r_angle_refined_deg 1.412 r_angle_other_deg 1.311 r_chiral_restr 0.073 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9434 Nucleic Acid Atoms Solvent Atoms 639 Heterogen Atoms 203
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing