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Crystal Structure of Human B-raf bound to a DFG-out Inhibitor TAK-632
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DBN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop, vapor diffusion 8.3 277 9.6 % PEG 8000, 0.8M LiCl, 100 mM Tris pH 8.3, sitting drop, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.5 64.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.495 α = 90 b = 111.495 β = 90 c = 145.487 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 2010-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.93 50 99.8 0.157 5.4 6.7 20307 20267
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.93 3 98.5 0.861 3.9 960
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 4DBN 2.93 35 20307 20089 1031 98.4 0.1965 0.1941 0.1955 0.2417 0.2447 RANDOM 79.5058
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] -0.89 -0.89 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.825 r_dihedral_angle_4_deg 18.188 r_dihedral_angle_3_deg 18.17 r_dihedral_angle_1_deg 5.896 r_angle_refined_deg 1.317 r_angle_other_deg 0.734 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.825 r_dihedral_angle_4_deg 18.188 r_dihedral_angle_3_deg 18.17 r_dihedral_angle_1_deg 5.896 r_angle_refined_deg 1.317 r_angle_other_deg 0.734 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4099 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 78
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction MOLREP phasing