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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 42.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.901 α = 90 b = 88.187 β = 91.12 c = 40.982 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 RAYONIX MX300HE 2011-06-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 1.76 50 97.4 58.15 6.2 27304
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 1.76 1.79
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 1.76 44.09 25832 1443 97.18 0.22607 0.22287 0.2277 0.24246 0.2435 RANDOM 33.304
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] -0.27 -0.87 -1.21 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_4_deg 14.583 r_dihedral_angle_3_deg 12.57 r_dihedral_angle_1_deg 5.756 r_long_range_B_refined 3.016 r_long_range_B_other 2.654 r_mcangle_it 2.243 r_mcangle_other 2.242 r_mcbond_it 1.836 r_scangle_other 1.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.386 r_dihedral_angle_4_deg 14.583 r_dihedral_angle_3_deg 12.57 r_dihedral_angle_1_deg 5.756 r_long_range_B_refined 3.016 r_long_range_B_other 2.654 r_mcangle_it 2.243 r_mcangle_other 2.242 r_mcbond_it 1.836 r_scangle_other 1.822 r_mcbond_other 1.816 r_scbond_it 1.57 r_scbond_other 1.57 r_angle_refined_deg 1.262 r_angle_other_deg 0.895 r_chiral_restr 0.071 r_bond_refined_d 0.007 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 2171 Nucleic Acid Atoms Solvent Atoms 195 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing