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Crystal structure of TTBK1 with a covalent compound GCL95
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZHQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 17% 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 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.641 α = 90 b = 39.954 β = 93.3 c = 166.667 γ = 90
Symmetry Space Group I 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 EIGER X 16M 2022-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999995 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 3 48.26 99.8 0.977 6 4.7 6759
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 3 3.18 0.772 1.7
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 3 48.26 6426 332 99.78 0.23429 0.23162 0.2384 0.28592 0.2881 RANDOM 36.71
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] -7.24 -0.2 1.68 5.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.754 r_dihedral_angle_3_deg 16.728 r_long_range_B_refined 10.671 r_long_range_B_other 10.67 r_dihedral_angle_1_deg 7.309 r_scangle_other 4.659 r_mcangle_it 4.643 r_mcangle_other 4.641 r_mcbond_it 2.72 r_mcbond_other 2.719
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.754 r_dihedral_angle_3_deg 16.728 r_long_range_B_refined 10.671 r_long_range_B_other 10.67 r_dihedral_angle_1_deg 7.309 r_scangle_other 4.659 r_mcangle_it 4.643 r_mcangle_other 4.641 r_mcbond_it 2.72 r_mcbond_other 2.719 r_scbond_it 2.645 r_scbond_other 2.644 r_angle_refined_deg 1.818 r_angle_other_deg 0.551 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 2379 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing