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Crystal structure of an inhibitor-bound Syk
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 278 10~20%(v/v) PEG3350, 100 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.13 42.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.933 α = 90 b = 88.267 β = 91.37 c = 41.078 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 270 2010-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 1.2398 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 92.7 33.21 7 10345
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44
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 4XG2 2.4 44.13 9770 559 92.57 0.19175 0.1895 0.1987 0.23015 0.2241 RANDOM 42.939
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] -0.31 -1.2 -2.14 2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.606 r_dihedral_angle_3_deg 14.906 r_dihedral_angle_4_deg 14.654 r_dihedral_angle_1_deg 6.123 r_long_range_B_refined 5.265 r_long_range_B_other 5.251 r_mcangle_it 3.239 r_mcangle_other 3.238 r_scangle_other 3.049 r_mcbond_it 1.899
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.606 r_dihedral_angle_3_deg 14.906 r_dihedral_angle_4_deg 14.654 r_dihedral_angle_1_deg 6.123 r_long_range_B_refined 5.265 r_long_range_B_other 5.251 r_mcangle_it 3.239 r_mcangle_other 3.238 r_scangle_other 3.049 r_mcbond_it 1.899 r_mcbond_other 1.894 r_scbond_it 1.722 r_scbond_other 1.721 r_angle_refined_deg 1.337 r_angle_other_deg 0.919 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.003 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2200 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing