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MerTK kinase domain with type 3 inhibitor from a DNA-encoded library
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other internal model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.3 mM protein co-crystallised with 0.5 mM compound (1 % DMSO) in 25 % PEG3350, 0.2 M MgCl2, 0.1 M PCTP pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.568 α = 90 b = 90.49 β = 99.37 c = 69.415 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 PILATUS 6M 2017-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
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 1.98 49.86 99.9 0.154 0.184 0.1 0.987 4.6 3.3 42994 23.45
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 1.98 2.03 99.9 1.235 1.478 0.804 0.556 3.2
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 internal model 1.98 39.48 41173 2053 95.5 0.215 0.214 0.2407 0.246 0.2769 RANDOM 36.83
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] 1.8252 0.7892 -0.4896 -1.3356
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.96 t_omega_torsion 2.42 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.96 t_omega_torsion 2.42 t_angle_deg 0.93 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4114 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 113
Software Software Software Name Purpose Aimless data scaling AMoRE phasing BUSTER refinement PDB_EXTRACT data extraction DIALS data reduction