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Crystal structure of TTBK1 in complex with VNG2.73 (compound 42)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 29% PEG 3350, 0.2M sodium acetate, 0.1M tris 8.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.915 α = 90 b = 39.519 β = 103.08 c = 49.037 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 EIGER2 X 16M 2021-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00002 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 2.13 47.77 97.1 0.07 0.081 0.03 0.998 13.4 7 17584
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 2.13 2.2 97.2 0.903 1.054 0.398 0.778 2 6.9
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 7jxx 2.13 47.77 16685 899 96.59 0.1903 0.1874 0.1944 0.2444 0.2521 RANDOM 49.496
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] 1.56 -2.17 2.11 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 21.594 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 8.14 r_angle_refined_deg 1.298 r_angle_other_deg 1.206 r_chiral_restr 0.061 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 21.594 r_dihedral_angle_3_deg 14.69 r_dihedral_angle_1_deg 8.14 r_angle_refined_deg 1.298 r_angle_other_deg 1.206 r_chiral_restr 0.061 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2380 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 29
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing