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Crystal structure of TTBK1 in complex with AMG28
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Q8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 14-23% PEG 3350, 0.2 M sodium acetate pH 7.0 and 0.1 M tris pH 7.5-9.0
Crystal Properties Matthews coefficient Solvent content 2.31 46.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 171.752 α = 90 b = 39.556 β = 103.23 c = 49.715 γ = 90
Symmetry Space Group C 1 2 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 2021-08-19 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) 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 1.85 48.4 100 0.086 0.102 0.039 0.999 13.4 6.7 28144
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 1.85 1.91 99.9 0.884 1.058 0.413 0.773 1.9 6.4
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 7q8w 1.85 46.78 26761 1382 99.95 0.1915 0.1903 0.2145 0.2053 RANDOM 30.351
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] -0.43 0.15 1.68 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 13.679 r_dihedral_angle_1_deg 7.658 r_angle_refined_deg 1.515 r_angle_other_deg 1.326 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.566 r_dihedral_angle_4_deg 17.081 r_dihedral_angle_3_deg 13.679 r_dihedral_angle_1_deg 7.658 r_angle_refined_deg 1.515 r_angle_other_deg 1.326 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2385 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 54
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing