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Furo[2,3-c]pyridine-based Indanone Oximes as Potent and Selective B-Raf Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 10% PEG 8K
100mM Hepes pH8.0
3% aminocaproic acid
10% glycerol
2.6mg/ml protein
500uM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.95 58.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.073 α = 90 b = 101.073 β = 90 c = 162.952 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 IMAGE PLATE RIGAKU RAXIS IV++ 2005-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 3.4 30 99.7 0.17 0.17 6.12 14.1 12196 12160
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) 3.4 3.6 99.7 0.395 0.381 2 14.5 1727
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 3D4Q 3.4 28.63 12196 11511 621 100 0.22671 0.22445 0.2103 0.2681 0.2533 RANDOM 45.714
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.532 r_dihedral_angle_3_deg 18.125 r_dihedral_angle_4_deg 16.198 r_dihedral_angle_1_deg 5.468 r_angle_refined_deg 1.136 r_scangle_it 0.943 r_mcangle_it 0.713 r_scbond_it 0.518 r_mcbond_it 0.389 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.532 r_dihedral_angle_3_deg 18.125 r_dihedral_angle_4_deg 16.198 r_dihedral_angle_1_deg 5.468 r_angle_refined_deg 1.136 r_scangle_it 0.943 r_mcangle_it 0.713 r_scbond_it 0.518 r_mcbond_it 0.389 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4200 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling