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Crystal structure of Casein Kinase I delta (CK1d) in complex with double phosphorylated p63 PAD2P 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 2.38 48.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.779 α = 90 b = 48.673 β = 109.93 c = 87.631 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 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 2.08 46.6 99.3 0.114 0.125 0.05 0.996 8.6 6 41053
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 2.08 2.19 99.6 0.83 0.907 0.36 0.865 2 6.2
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 2.08 46.6 39030 2017 99.19 0.1775 0.1754 0.1855 0.2182 0.2235 RANDOM 44.001
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] -1.45 0.9 -1.24 1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_4_deg 17.734 r_dihedral_angle_3_deg 15.054 r_dihedral_angle_1_deg 7.091 r_angle_refined_deg 1.323 r_angle_other_deg 1.261 r_chiral_restr 0.068 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.198 r_dihedral_angle_4_deg 17.734 r_dihedral_angle_3_deg 15.054 r_dihedral_angle_1_deg 7.091 r_angle_refined_deg 1.323 r_angle_other_deg 1.261 r_chiral_restr 0.068 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4935 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 127
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing