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Crystal structure of Casein Kinase I delta (CK1d) in complex with monophosphorylated p63 PAD1P 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 2.4 48.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.937 α = 90 b = 48.924 β = 109.72 c = 85.199 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 PILATUS3 6M 2018-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.03320 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.05 49.26 99.4 0.117 0.131 0.057 0.996 8.3 5 42000
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 2.05 2.12 99.5 0.784 0.876 0.382 0.837 2 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 4HNF 2.05 49.26 39925 2074 99.29 0.2131 0.2108 0.2215 0.257 0.2634 RANDOM 50.924
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] -3.58 1.77 -2.25 3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.449 r_dihedral_angle_4_deg 20.683 r_dihedral_angle_3_deg 15.311 r_dihedral_angle_1_deg 7.448 r_angle_refined_deg 1.278 r_angle_other_deg 1.166 r_chiral_restr 0.058 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.449 r_dihedral_angle_4_deg 20.683 r_dihedral_angle_3_deg 15.311 r_dihedral_angle_1_deg 7.448 r_angle_refined_deg 1.278 r_angle_other_deg 1.166 r_chiral_restr 0.058 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4697 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 100
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing