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Crystal structure of phosphorylated pT220 Casein Kinase I delta (CK1d), conformation 2 and 3
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 277.15 12% PEG 3350 and 0.1 M ammonium citrate
Crystal Properties Matthews coefficient Solvent content 2.04 39.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.542 α = 90 b = 64.254 β = 90 c = 163.966 γ = 90
Symmetry Space Group P 21 21 21
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 2021-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00009 SLS X06DA
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 1.7 44.83 100 0.095 0.104 0.031 0.999 16 10.9 63264
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 1.7 1.74 100 0.978 1.084 0.325 0.801 2.4 10.7
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 1.7 44.83 60063 3122 99.99 0.1726 0.1708 0.1824 0.2079 0.2139 RANDOM 26.34
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] 1.28 -0.61 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.066 r_dihedral_angle_4_deg 18.295 r_dihedral_angle_3_deg 13.617 r_dihedral_angle_1_deg 7.473 r_angle_refined_deg 1.484 r_angle_other_deg 1.388 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.066 r_dihedral_angle_4_deg 18.295 r_dihedral_angle_3_deg 13.617 r_dihedral_angle_1_deg 7.473 r_angle_refined_deg 1.484 r_angle_other_deg 1.388 r_chiral_restr 0.082 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4664 Nucleic Acid Atoms Solvent Atoms 429 Heterogen Atoms 105
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing