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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 2.11 41.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.964 α = 99.97 b = 42.212 β = 90.5 c = 87.72 γ = 101.05
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 RIGAKU JUPITER 210 2011-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0000 SPring-8 BL26B1
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 97 23.83 3.7 20930
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XG2 2.4 35.112 19912 1010 96.03 0.24871 0.24739 0.27487 0.2624 RANDOM 56.362
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] -0.83 -1.97 -0.6 3.93 0.27 -2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.889 r_dihedral_angle_4_deg 17.548 r_dihedral_angle_3_deg 15.144 r_long_range_B_refined 7.607 r_long_range_B_other 7.607 r_dihedral_angle_1_deg 6.688 r_scangle_other 5.076 r_mcangle_it 5.021 r_mcangle_other 5.021 r_mcbond_it 3.258
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.889 r_dihedral_angle_4_deg 17.548 r_dihedral_angle_3_deg 15.144 r_long_range_B_refined 7.607 r_long_range_B_other 7.607 r_dihedral_angle_1_deg 6.688 r_scangle_other 5.076 r_mcangle_it 5.021 r_mcangle_other 5.021 r_mcbond_it 3.258 r_mcbond_other 3.247 r_scbond_it 3.243 r_scbond_other 3.243 r_angle_refined_deg 1.534 r_angle_other_deg 1.065 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.004 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 4146 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing