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DLK in complex with inhibitor 5-(1-isopropyl-5-(1-(oxetan-3-yl)piperidin-4-yl)-1H-pyrazol-3-yl)-3-(trifluoromethyl)pyridin-2-amine (compound 7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 293 20% PEG 3350, 0.2 M Mg Acetate, 0.1 M Hepes pH 7.7
Crystal Properties Matthews coefficient Solvent content 1.93 36.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.29 α = 90 b = 39.463 β = 104.81 c = 60.113 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 CCD ADSC QUANTUM 315 2012-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.958 39.463 99.5 0.099 0.135 0.071 11.5 3.6 5586 5586 52.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.96 3.12 100 0.312 0.312 0.409 0.212 2.5 3.6
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 5CEN 2.96 35.79 5569 315 99.41 0.1743 0.1695 0.1718 0.2637 0.2674 RANDOM 34.14
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] 10.0096 8.3683 1.1953 -11.2049
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.71 t_omega_torsion 2.3 t_angle_deg 1.02 t_bond_d 0.009 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 20.71 t_omega_torsion 2.3 t_angle_deg 1.02 t_bond_d 0.009 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 2156 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 29
Software Software Software Name Purpose SCALA data scaling BUSTER refinement PDB_EXTRACT data extraction PHASER phasing XDS data reduction