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Crystal structure of MerTK Kinase domain with BMS794833
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 Protein concentration 25 mg/mL
Protein storage buffer:
Tris-HCl pH 8.0, 500 mM NaCl, 1 mM Tris(2-carboxyethyl)phosphine Hydrochloride (TCEP)
Mother Liquor: 0.1 M Tris-HCl pH 8.5, 4.3 M NaCl
Protein: Reservoir: Apo-Microseed = 300: 300: 100 nL or 400: 400: 100 nL
Co-crystalization
2mM compound preincubation: 2Hours in ICE
Cryoprotectant solution:
0.1 M Tris-HCl pH 8.5, 2.5 M NaCl, 20% DMSO, 10 mM compounds
Crystal Properties Matthews coefficient Solvent content 2.11 41.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.127 α = 90 b = 92.533 β = 90 c = 71.435 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M 2021-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.979 PAL/PLS 11C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.16 50 98.5 0.081 0.088 0.034 0.985 23.2 6.8 16509 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.2 80.5 0.478 0.528 0.218 0.931 2.1 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7aax 2.16 38.71 1.36 16477 1648 98.67 0.2125 0.208 0.2112 0.2523 0.2554 47.47
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.7364 f_angle_d 1.0447 f_chiral_restr 0.0592 f_bond_d 0.0081 f_plane_restr 0.0066
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2167 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement PHASER phasing HKL-2000 data scaling HKL-2000 data reduction PDB_EXTRACT data extraction