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Crystal structure of Casein Kinase I delta (CK1d) with alphaG-in conformation
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 5.5 277.15 18% PEG 6000, 1 M LiCl and 0.1 M citrate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.029 α = 90 b = 73.377 β = 103.64 c = 90.608 γ = 90
Symmetry Space Group P 1 21 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 EIGER2 X 16M 2021-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00002 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 2.4 44.03 94.5 0.169 0.213 0.095 0.98 7 4.7 23044
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 2.4 2.53 95 0.808 1.021 0.455 0.697 1.7 4.5
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 2.4 44.03 22004 1027 93.67 0.2251 0.223 0.2261 0.2684 0.2727 RANDOM 43.573
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] -1.13 -0.13 1.8 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.34 r_dihedral_angle_4_deg 19.101 r_dihedral_angle_3_deg 16.608 r_dihedral_angle_1_deg 7.979 r_angle_refined_deg 1.238 r_angle_other_deg 1.118 r_chiral_restr 0.049 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.34 r_dihedral_angle_4_deg 19.101 r_dihedral_angle_3_deg 16.608 r_dihedral_angle_1_deg 7.979 r_angle_refined_deg 1.238 r_angle_other_deg 1.118 r_chiral_restr 0.049 r_gen_planes_refined 0.01 r_bond_refined_d 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 4776 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 46
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing