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Structure of the B-Raf kinase domain bound to SB-590885
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 8% PEG 8000, 0.4 M LiCl, 0.1 M Tris, 0.02 M Bis-Tris Propane, 15% glycerol, 1 mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 18K, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.638 α = 90 b = 95.638 β = 90 c = 159.222 γ = 90
Symmetry Space Group P 41 21 2
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 315 2005-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97946 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 46.42 98.4 0.227 0.227 2.5 6 16843 16667
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) 2.9 3.06 98.4 0.489 0.489 1.5 6.2 2360
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.9 46.42 16653 16653 840 97.87 0.203 0.203 0.199 0.198 0.291 0.2869 RANDOM 26.017
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] -0.39 -0.39 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.731 r_dihedral_angle_4_deg 21.658 r_dihedral_angle_3_deg 21.266 r_dihedral_angle_1_deg 8.557 r_scangle_it 3.132 r_angle_refined_deg 2.219 r_scbond_it 1.947 r_mcangle_it 1.595 r_mcbond_it 0.888 r_nbtor_refined 0.342
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.731 r_dihedral_angle_4_deg 21.658 r_dihedral_angle_3_deg 21.266 r_dihedral_angle_1_deg 8.557 r_scangle_it 3.132 r_angle_refined_deg 2.219 r_scbond_it 1.947 r_mcangle_it 1.595 r_mcbond_it 0.888 r_nbtor_refined 0.342 r_nbd_refined 0.276 r_symmetry_vdw_refined 0.23 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.146 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4134 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 68
Software Software Software Name Purpose SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling