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Human jak1 kinase domain in complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 278 27% (m/v) PEG6000, 0.1 M MES/NaOH pH 6.0 and 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.987 α = 90 b = 170.327 β = 94.06 c = 45.026 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 X 1M 2013-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
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 1.7 85.16 96.4 0.05 10.94 2.3 68097
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 1.7 1.95 96.4 0.44 2.3
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 3EYG 1.7 85.16 64937 3160 96.37 0.19229 0.18879 0.1976 0.26186 0.2704 RANDOM 33.544
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] -1.8 -0.64 2.3 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.618 r_sphericity_free 29.031 r_dihedral_angle_4_deg 16.29 r_sphericity_bonded 15.754 r_dihedral_angle_3_deg 12.451 r_rigid_bond_restr 8.053 r_dihedral_angle_1_deg 5.693 r_angle_other_deg 1.815 r_angle_refined_deg 1.297 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.618 r_sphericity_free 29.031 r_dihedral_angle_4_deg 16.29 r_sphericity_bonded 15.754 r_dihedral_angle_3_deg 12.451 r_rigid_bond_restr 8.053 r_dihedral_angle_1_deg 5.693 r_angle_other_deg 1.815 r_angle_refined_deg 1.297 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4617 Nucleic Acid Atoms Solvent Atoms 346 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement AMoRE phasing