8C7Y

Crystal structure of BRAF V600E in complex with a hybrid compound 6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental model4WO5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.1513% PEG3350, 0.2M sodium nitrate, 5% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.1643.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.269α = 90
b = 97.739β = 90
c = 115.279γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97624DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.6574.5599.40.0670.0710.0240.99919.38.167419
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.740.2450.2660.1020.9586.46.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6574.5564035331399.350.153440.152310.17504RANDOM18.456
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]
-0.67-0.351.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_4_deg17.415
r_dihedral_angle_3_deg11.527
r_long_range_B_other6.297
r_long_range_B_refined6.296
r_dihedral_angle_1_deg5.868
r_scangle_other2.639
r_mcangle_it2.06
r_mcangle_other2.06
r_scbond_it1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.289
r_dihedral_angle_4_deg17.415
r_dihedral_angle_3_deg11.527
r_long_range_B_other6.297
r_long_range_B_refined6.296
r_dihedral_angle_1_deg5.868
r_scangle_other2.639
r_mcangle_it2.06
r_mcangle_other2.06
r_scbond_it1.63
r_scbond_other1.629
r_angle_refined_deg1.627
r_angle_other_deg1.497
r_mcbond_it1.214
r_mcbond_other1.213
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.012
r_bond_other_d0.009
r_gen_planes_other0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4261
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing