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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 2.07 40.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.269 α = 89.99 b = 41.501 β = 90.01 c = 85.091 γ = 98.9
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 2.8 39.78 99.7 30.18 5.7 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 2.8 2.85
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 2.8 39.78 11722 569 91.9 0.217 0.217 0.2202 0.227 0.2373 RANDOM 43.35
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] -2.25 -1.61 0.05 5.08 0.09 -2.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 15.535 r_dihedral_angle_3_deg 13.419 r_dihedral_angle_1_deg 5.615 r_long_range_B_refined 2.366 r_long_range_B_other 2.365 r_angle_refined_deg 1.565 r_mcangle_it 1.354 r_mcangle_other 1.354 r_angle_other_deg 0.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.069 r_dihedral_angle_4_deg 15.535 r_dihedral_angle_3_deg 13.419 r_dihedral_angle_1_deg 5.615 r_long_range_B_refined 2.366 r_long_range_B_other 2.365 r_angle_refined_deg 1.565 r_mcangle_it 1.354 r_mcangle_other 1.354 r_angle_other_deg 0.877 r_scangle_other 0.844 r_mcbond_it 0.724 r_mcbond_other 0.724 r_scbond_it 0.417 r_scbond_other 0.417 r_chiral_restr 0.058 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 4318 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 70
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing REFMAC refinement