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Non-oxime pyrazole based inhibitors of B-Raf kinase
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 7.5% PEG 3350
100mM Tris pH8.0
10% Tacsimate
10% glycerol
1.6mg/ml protein
500uM inhibitor
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.98 α = 90 b = 94.98 β = 90 c = 161.73 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++ 2005-03-03 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 3.6 30 98.7 0.185 0.18 5.3 13.9 9044 8936
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 3.6 3.8 98.7 0.35 0.34 2.3 2.3 1279
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 3.6 29.53 9044 8434 491 100 0.28041 0.27733 0.26 0.33463 0.3098 RANDOM 42.539
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] 0.68 0.68 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_4_deg 11.072 r_dihedral_angle_1_deg 4.108 r_angle_refined_deg 1.061 r_mcangle_it 0.274 r_scangle_it 0.161 r_mcbond_it 0.153 r_scbond_it 0.088 r_chiral_restr 0.057
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_4_deg 11.072 r_dihedral_angle_1_deg 4.108 r_angle_refined_deg 1.061 r_mcangle_it 0.274 r_scangle_it 0.161 r_mcbond_it 0.153 r_scbond_it 0.088 r_chiral_restr 0.057 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 58
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling