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Crystal structure of Casein kinase I isoform delta (CK1 delta) complexed with SR4133 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 5.9 277.15 25% PEG3350, 0.2M sodium sulfate, 0.1M citrate pH 5.9
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.106 α = 90 b = 74.072 β = 103.18 c = 88.967 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 PILATUS3 6M 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.45 86.622 99 0.171 0.188 0.077 0.978 6.5 5.7 108708
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 1.45 1.53 97.1 0.439 0.439 0.486 0.204 0.858 3.1 5.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4HNF 1.45 86.62 103364 5329 99.01 0.1566 0.1554 0.1783 0.2061 RANDOM 16.295
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] -0.17 0.04 0.2 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.689 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_3_deg 12.23 r_dihedral_angle_1_deg 5.947 r_angle_refined_deg 1.615 r_angle_other_deg 1.521 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.689 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_3_deg 12.23 r_dihedral_angle_1_deg 5.947 r_angle_refined_deg 1.615 r_angle_other_deg 1.521 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4775 Nucleic Acid Atoms Solvent Atoms 776 Heterogen Atoms 103
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing