3TV4

Human B-Raf Kinase Domain in Complex with an Bromopyridine Benzamide Inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293PEG 8000, Tris pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1761.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.966α = 90
b = 107.966β = 90
c = 153.142γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Osmic confocal2007-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
13.43099.50.1183.11299312929
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.43.5899.90.36723.11835

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3.43012890122616291000.243790.240530.30746RANDOM50.09
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]
-0.42-0.420.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.59
r_dihedral_angle_3_deg20.775
r_dihedral_angle_4_deg18.004
r_dihedral_angle_1_deg6.061
r_scangle_it1.628
r_angle_refined_deg1.347
r_mcangle_it0.983
r_scbond_it0.884
r_mcbond_it0.531
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.59
r_dihedral_angle_3_deg20.775
r_dihedral_angle_4_deg18.004
r_dihedral_angle_1_deg6.061
r_scangle_it1.628
r_angle_refined_deg1.347
r_mcangle_it0.983
r_scbond_it0.884
r_mcbond_it0.531
r_chiral_restr0.096
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms4326
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
CNXrefinement
CrystalCleardata collection
MOSFLMdata reduction
SCALAdata scaling
CNXphasing