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TTK kinase domain in complex with BAY 1217389
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 32 - 37% PEG400 (Acros, Geel, Belgium), 0.1 M Na/K phosphate pH 6.3 and 250 mM NaCl.pH 6.3
Crystal Properties Matthews coefficient Solvent content 3.05 59.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.45 α = 90 b = 109.78 β = 90 c = 114.33 γ = 90
Symmetry Space Group I 2 2 2
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 2M 2016-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 79.19 99.4 0.093 0.057 0.991 7.1 4.3 11158
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.99 99.1 0.936 0.562 0.611 1.3 4.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5N7V 2.8 79.19 10516 530 98.2 0.20962 0.20593 0.2177 0.28967 0.2831 RANDOM 89.214
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] 0.21 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.471 r_dihedral_angle_4_deg 19.921 r_dihedral_angle_3_deg 18.51 r_dihedral_angle_1_deg 7.651 r_angle_refined_deg 1.863 r_angle_other_deg 0.958 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.471 r_dihedral_angle_4_deg 19.921 r_dihedral_angle_3_deg 18.51 r_dihedral_angle_1_deg 7.651 r_angle_refined_deg 1.863 r_angle_other_deg 0.958 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2109 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling AMoRE phasing