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Crystal structure of TTBK2 in complex with VNG1.63 (compound 32)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U0K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 1.6M Na/K phosphate pH 7, 5% Glycerol, 0.1M tris 8.0
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.906 α = 90 b = 114.82 β = 90 c = 120.703 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 EIGER2 X 16M 2021-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA
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 1.6 46.4 99.8 0.097 0.106 0.033 0.998 16.9 10.1 102884
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 1.6 1.64 99.9 0.99 1.101 0.334 0.783 2.4 10.6
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 6u0k 1.6 46.4 97779 5022 99.66 0.1915 0.19 0.2009 0.2202 0.2294 RANDOM 21.648
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 -0.11 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.046 r_dihedral_angle_4_deg 13.188 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_1_deg 6.581 r_angle_refined_deg 1.574 r_angle_other_deg 1.43 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.046 r_dihedral_angle_4_deg 13.188 r_dihedral_angle_3_deg 12.245 r_dihedral_angle_1_deg 6.581 r_angle_refined_deg 1.574 r_angle_other_deg 1.43 r_chiral_restr 0.098 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4765 Nucleic Acid Atoms Solvent Atoms 789 Heterogen Atoms 60
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing