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Crystal Structure of the Jak3 Kinase Domain Covalently Bound to N-(3-(((5-chloro-2-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)pyrimidin-4-yl)amino)methyl)phenyl)acrylamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M Bis-tris pH 6.5, 16% PEG 3350, 0.2 M ammonium sulfate, 5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.71 54.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.625 α = 92.64 b = 68.207 β = 93.06 c = 93.13 γ = 86.2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2014-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.9 92.91 97 0.13 7.1 2.2 30357 64.79
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 1YVJ 2.9 92.91 30356 1495 96.98 0.204 0.2021 0.2401 0.2342 RANDOM 65.05
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] 8.807 -4.2871 4.6577 -14.5404 17.0635 5.7334
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.2 t_omega_torsion 2.1 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.2 t_omega_torsion 2.1 t_angle_deg 1 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 8711 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 144
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing