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Crystal structure of CK1 delta in complex with VN725
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RU8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 20% PEG 3350, 0.1M sodium sulfate, 0.1M citrate 5.0
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.208 α = 70.84 b = 84.949 β = 74.08 c = 90.07 γ = 86.93
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 PILATUS 6M 2018-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 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 2.4 49.74 92.9 0.122 0.172 0.097 0.984 5.9 2.9 48143
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 96.6 0.376 0.539 0.307 0.845 2.2 2.8
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 6RU8 2.4 49.74 45677 2272 92.54 0.2406 0.2385 0.2466 0.2816 0.2847 RANDOM 32.3
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 0.64 0.07 2.17 -1.66 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.494 r_dihedral_angle_4_deg 20.199 r_dihedral_angle_3_deg 16.574 r_dihedral_angle_1_deg 7.276 r_angle_refined_deg 1.107 r_angle_other_deg 0.81 r_chiral_restr 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.494 r_dihedral_angle_4_deg 20.199 r_dihedral_angle_3_deg 16.574 r_dihedral_angle_1_deg 7.276 r_angle_refined_deg 1.107 r_angle_other_deg 0.81 r_chiral_restr 0.058 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9270 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 198
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing