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Crystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated p63 PAD3P peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HNF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 10-20% PEG 3350, 0.1-0.2 M sodium sulfate and 0.1 M citrate, pH 4.6-5.9
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.727 α = 108.6 b = 84.131 β = 105.83 c = 89.287 γ = 91.57
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 EIGER X 16M 2018-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 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 1.92 48.84 92.2 0.096 0.111 0.056 0.994 7.2 3.9 90338
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 1.92 1.99 91.5 0.676 0.785 0.397 0.843 2.1 3.9
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 4HNF 1.92 48.84 85820 4513 92.16 0.1737 0.1718 0.1799 0.2106 0.2159 RANDOM 37.523
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] -0.46 0.14 0.05 1.41 1.22 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.024 r_dihedral_angle_4_deg 18.973 r_dihedral_angle_3_deg 13.952 r_dihedral_angle_1_deg 6.725 r_angle_refined_deg 1.288 r_angle_other_deg 1.273 r_chiral_restr 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.024 r_dihedral_angle_4_deg 18.973 r_dihedral_angle_3_deg 13.952 r_dihedral_angle_1_deg 6.725 r_angle_refined_deg 1.288 r_angle_other_deg 1.273 r_chiral_restr 0.069 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9796 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 197
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing