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Crystal structure of JAK3 in complex with Compound 11 (FM481)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LWM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 24-30% PEG 3350, 0.1 M MES, pH 5.5-6.0 and 0.1-0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 1.93 36.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.951 α = 90 b = 61.358 β = 92.37 c = 100.434 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 PILATUS3 6M 2016-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.92 52.35 99.9 0.146 4.9 4.1 39077
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 2.02 99.5 0.528 2 4
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 5lwm 1.92 52.35 37123 1928 99.88 0.22839 0.22599 0.27339 0.2921 RANDOM 26.804
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] -3.04 0.25 0.02 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.224 r_dihedral_angle_4_deg 16.848 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_1_deg 6.267 r_long_range_B_refined 4.917 r_long_range_B_other 4.917 r_scangle_other 2.431 r_mcangle_it 2.095 r_mcangle_other 2.095 r_angle_refined_deg 1.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.224 r_dihedral_angle_4_deg 16.848 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_1_deg 6.267 r_long_range_B_refined 4.917 r_long_range_B_other 4.917 r_scangle_other 2.431 r_mcangle_it 2.095 r_mcangle_other 2.095 r_angle_refined_deg 1.662 r_scbond_it 1.476 r_scbond_other 1.476 r_mcbond_it 1.233 r_mcbond_other 1.233 r_angle_other_deg 1.226 r_chiral_restr 0.1 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4566 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing