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CK2 alpha bound to chemical probe SGC-CK2-1 derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YUL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M bis-tris pH 5.5
23-26% (v/v) PEG 3350
0.2 M ammonia sulphate
Crystal Properties Matthews coefficient Solvent content 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.352 α = 90 b = 126.352 β = 90 c = 124.514 γ = 90
Symmetry Space Group P 43 21 2
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 2M-F 2020-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99999 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 44.67 100 0.056 0.998 12.7 13.2 35531
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.415 0.845 2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6yul 2.5 44.67 35475 1850 99.969 0.217 0.215 0.2189 0.2501 0.2516 39.771
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] 2.362 2.362 -4.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.021 r_dihedral_angle_4_deg 18.479 r_dihedral_angle_3_deg 15.502 r_dihedral_angle_1_deg 6.248 r_lrange_it 4.587 r_lrange_other 4.525 r_mcangle_it 2.667 r_mcangle_other 2.667 r_scangle_other 2.563 r_scangle_it 2.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.021 r_dihedral_angle_4_deg 18.479 r_dihedral_angle_3_deg 15.502 r_dihedral_angle_1_deg 6.248 r_lrange_it 4.587 r_lrange_other 4.525 r_mcangle_it 2.667 r_mcangle_other 2.667 r_scangle_other 2.563 r_scangle_it 2.56 r_mcbond_it 1.556 r_mcbond_other 1.556 r_angle_other_deg 1.49 r_scbond_it 1.482 r_scbond_other 1.482 r_angle_refined_deg 1.406 r_nbd_refined 0.218 r_nbd_other 0.211 r_symmetry_nbd_refined 0.187 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.124 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.08 r_ext_dist_refined_d 0.051 r_bond_refined_d 0.009 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 5415 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing