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STE20-like serine/threonine-protein kinase (SLK) in complex with Tivozanib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 20% PEG 3350
0.2M Na2SO4
10% Ethylene Glycol
0.1M bis-tris propane 7.5
Crystal Properties Matthews coefficient Solvent content 2.97 58.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.012 α = 90 b = 107.28 β = 95.32 c = 129.4 γ = 90
Symmetry Space Group P 1 21 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 2022-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000031 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 2.6 49.52 99.2 0.134 0.145 0.054 0.997 11 7.1 48206
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 2.6 2.69 99.6 1.025 1.103 0.405 0.769 7.3
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 6HVD 2.6 48.73 45795 2391 99.08 0.2236 0.2219 0.2551 0.2455 RANDOM 53.733
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] -1.79 -0.43 1.41 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.293 r_dihedral_angle_2_deg 7.705 r_dihedral_angle_1_deg 6.102 r_angle_refined_deg 1.401 r_angle_other_deg 0.478 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8477 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction