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Crystal structure of JAK1 JH1 domain in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 0.1 M MES pH 5-6 and 25-35% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.038 α = 90 b = 174.03 β = 94.5 c = 44.893 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 315r 2011-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979500 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.75 87.01 96.2 0.05 0.059 17.8 3.5 60553
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.82 0.547 0.657
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 87.01 60553 2941 96.35 0.20988 0.20791 0.2162 0.2496 0.2569 RANDOM 35.589
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] -0.93 0.31 -0.56 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.925 r_dihedral_angle_4_deg 18.534 r_dihedral_angle_3_deg 12.29 r_dihedral_angle_1_deg 6.083 r_scangle_it 5.581 r_scbond_it 4.035 r_mcangle_it 2.847 r_mcbond_it 1.929 r_angle_refined_deg 1.33 r_angle_other_deg 1.285
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.925 r_dihedral_angle_4_deg 18.534 r_dihedral_angle_3_deg 12.29 r_dihedral_angle_1_deg 6.083 r_scangle_it 5.581 r_scbond_it 4.035 r_mcangle_it 2.847 r_mcbond_it 1.929 r_angle_refined_deg 1.33 r_angle_other_deg 1.285 r_mcbond_other 0.484 r_symmetry_vdw_refined 0.245 r_symmetry_vdw_other 0.207 r_nbd_refined 0.186 r_nbd_other 0.167 r_nbtor_refined 0.165 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.076 r_nbtor_other 0.069 r_symmetry_metal_ion_refined 0.036 r_metal_ion_refined 0.017 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4682 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing