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Crystal Structure of Human Kinase Domain of B-raf with a DFG-out Inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 277 7.8% PEG 8000, 0.8M LiCl, 100 mM Tris, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.41 63.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.968 α = 90 b = 109.968 β = 90 c = 145.973 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 92 CCD MARMOSAIC 300 mm CCD 2008-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0 APS 23-ID-B
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 2.95 40 99.3 0.186 4.8 20800 19439 1.8 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2.95 30 1.8 19355 19355 986 99.44 0.1999 0.1976 0.2033 0.2431 0.2481 RANDOM 34.0008
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] 0.75 0.75 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.215 r_dihedral_angle_3_deg 17.573 r_dihedral_angle_4_deg 14.704 r_dihedral_angle_1_deg 5.519 r_scangle_it 1.317 r_angle_refined_deg 1.079 r_angle_other_deg 0.795 r_scbond_it 0.748 r_mcangle_it 0.482 r_mcbond_it 0.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.215 r_dihedral_angle_3_deg 17.573 r_dihedral_angle_4_deg 14.704 r_dihedral_angle_1_deg 5.519 r_scangle_it 1.317 r_angle_refined_deg 1.079 r_angle_other_deg 0.795 r_scbond_it 0.748 r_mcangle_it 0.482 r_mcbond_it 0.242 r_chiral_restr 0.059 r_mcbond_other 0.034 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4126 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling