6NVH

FGFR4 complex with N-(2-((5-((2,6-dichloro-3,5-dimethoxybenzyl)oxy)pyrimidin-2-yl)amino)-3-methylphenyl)acrylamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XCU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP291100mM Bis-tris pH 4.5, 200mM lithium sulphate, 12% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.127α = 90
b = 64.127β = 90
c = 181.924γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.945.521000.0230.99816.813.13098137.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9499.90.580.6231.511.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4XCU1.945.5229402149799.980.213260.212250.23364RANDOM39.829
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]
0.710.71-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.953
r_dihedral_angle_4_deg17.815
r_dihedral_angle_3_deg12.281
r_long_range_B_refined6.401
r_long_range_B_other6.4
r_dihedral_angle_1_deg5.99
r_scangle_other4.297
r_mcangle_it3.842
r_mcangle_other3.841
r_scbond_it2.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.953
r_dihedral_angle_4_deg17.815
r_dihedral_angle_3_deg12.281
r_long_range_B_refined6.401
r_long_range_B_other6.4
r_dihedral_angle_1_deg5.99
r_scangle_other4.297
r_mcangle_it3.842
r_mcangle_other3.841
r_scbond_it2.69
r_scbond_other2.689
r_mcbond_it2.531
r_mcbond_other2.53
r_angle_refined_deg1.29
r_angle_other_deg1.237
r_chiral_restr0.066
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2058
Nucleic Acid Atoms
Solvent Atoms106
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing