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Crystal structure of CSNK1G2 with a covalent compound GCL47
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 12% PEG Smear Medium, 0.1 M HEPES pH 7.0, 0.05 M ammonium acetate, and 0.15 M magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 2.83 56.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.765 α = 90 b = 96.11 β = 90 c = 184.046 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2023-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.9 48.1 100 0.999 12.4 13.6 37325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.03 100 0.81 1.9 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.9 48.1 35799 1830 99.96 0.23394 0.231 0.2342 0.29043 0.2908 RANDOM 108.804
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] -5.05 13.8 -8.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.223 r_long_range_B_refined 19.999 r_long_range_B_other 19.999 r_dihedral_angle_3_deg 18.42 r_scangle_other 14.838 r_mcangle_it 13.936 r_mcangle_other 13.935 r_scbond_it 9.858 r_scbond_other 9.858 r_mcbond_it 9.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.223 r_long_range_B_refined 19.999 r_long_range_B_other 19.999 r_dihedral_angle_3_deg 18.42 r_scangle_other 14.838 r_mcangle_it 13.936 r_mcangle_other 13.935 r_scbond_it 9.858 r_scbond_other 9.858 r_mcbond_it 9.416 r_mcbond_other 9.415 r_dihedral_angle_1_deg 6.908 r_angle_refined_deg 1.429 r_angle_other_deg 0.504 r_chiral_restr 0.067 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9443 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing