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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 4GX2
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 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.219 α = 90 b = 85.056 β = 98.8 c = 41.749 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 2010-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.0000 PAL/PLS 5C (4A)
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 2.3 50 98.3 24.13 3.9 12408
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 2.3 2.34
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 4GX2 2.3 42.53 11779 608 99.43 0.19522 0.19352 0.205 0.22843 0.2265 RANDOM 45.297
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] -2.75 -1.2 -3 5.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.711 r_dihedral_angle_4_deg 17.446 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 5.796 r_long_range_B_refined 5.455 r_long_range_B_other 5.422 r_mcangle_it 3.315 r_mcangle_other 3.315 r_scangle_other 3.283 r_mcbond_it 1.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.711 r_dihedral_angle_4_deg 17.446 r_dihedral_angle_3_deg 14.372 r_dihedral_angle_1_deg 5.796 r_long_range_B_refined 5.455 r_long_range_B_other 5.422 r_mcangle_it 3.315 r_mcangle_other 3.315 r_scangle_other 3.283 r_mcbond_it 1.963 r_mcbond_other 1.959 r_scbond_it 1.908 r_scbond_other 1.905 r_angle_refined_deg 1.202 r_angle_other_deg 0.886 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2150 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing