☰ Navigation Tabs
Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor
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 20% PEG3350, 0.1M succinic acid
Crystal Properties Matthews coefficient Solvent content 2.27 45.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.04 α = 90 b = 53.55 β = 113.45 c = 72.17 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 2M 2013-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.4 66.209 96.7 0.051 0.06 0.031 0.998 12 3.6 58592
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 97.5 0.462 0.462 0.546 0.286 0.87 2.4 3.5
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 4HNF 1.4 29.63 55619 2972 96.43 0.1442 0.1419 0.1423 0.1854 0.187 RANDOM 23.78
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] 0.33 -0.31 -1.13 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.254 r_dihedral_angle_3_deg 13.003 r_sphericity_bonded 12.768 r_dihedral_angle_4_deg 12.279 r_rigid_bond_restr 8.718 r_dihedral_angle_1_deg 6.161 r_angle_refined_deg 1.656 r_angle_other_deg 0.852 r_chiral_restr 0.106 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.254 r_dihedral_angle_3_deg 13.003 r_sphericity_bonded 12.768 r_dihedral_angle_4_deg 12.279 r_rigid_bond_restr 8.718 r_dihedral_angle_1_deg 6.161 r_angle_refined_deg 1.656 r_angle_other_deg 0.852 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2409 Nucleic Acid Atoms Solvent Atoms 381 Heterogen Atoms 78
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing