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Crystal structure of spleen tyrosine kinase (SYK) in complex with a diaminopyrimidine carboxamide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other OTHER IN-HOUSE COORDINATES
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 20% PEG3350, 0.2M Na-K-Phosphate, 0.1M Bis-Tris-Propane pH 6.5, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.124 α = 99.68 b = 42.316 β = 90.16 c = 87.621 γ = 100.19
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 2010-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9763 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.95 39.47 94.7 0.052 11.1 1.9 38589 38589 25.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.06 94.7 0.402 0.402 1.7 1.9 5634
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 FOURIER SYNTHESIS THROUGHOUT OTHER IN-HOUSE COORDINATES 1.95 20 38566 1929 100 0.1875 0.1846 0.1909 0.241 0.2449 RANDOM 35.6065
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] -0.71 -1.13 0.19 1.61 0.69 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 16.99 r_dihedral_angle_3_deg 13.965 r_dihedral_angle_1_deg 4.399 r_scangle_it 4.399 r_scbond_it 2.875 r_mcangle_it 2.187 r_angle_refined_deg 1.378 r_mcbond_it 1.218 r_angle_other_deg 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.25 r_dihedral_angle_4_deg 16.99 r_dihedral_angle_3_deg 13.965 r_dihedral_angle_1_deg 4.399 r_scangle_it 4.399 r_scbond_it 2.875 r_mcangle_it 2.187 r_angle_refined_deg 1.378 r_mcbond_it 1.218 r_angle_other_deg 0.881 r_mcbond_other 0.245 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4292 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms 74
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction REFMAC phasing