7KIE

Crystal structure of FGFR2 kinase domain gatekeeper mutant V564F in complex with covalent compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RI1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP429815% w/v PEG 8000, 0.1M Sodium Citrate pH 4.0
Crystal Properties
Matthews coefficientSolvent content
2.8456.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.3α = 90
b = 116.91β = 90
c = 64.67γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 R CdTe 300K2020-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X17B10.92009NSLSX17B1

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
12.4756.591000.1520.1630.060.99710.47.329660
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)
12.472.5399.91.2151.310.4860.5957.2

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 REPLACEMENTTHROUGHOUT3RI12.4750.0128141147199.940.2020.20060.2293RANDOM52.7
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]
-0.58-0.431.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.193
r_dihedral_angle_4_deg20.322
r_dihedral_angle_3_deg17.695
r_dihedral_angle_1_deg6.976
r_angle_refined_deg1.37
r_chiral_restr0.101
r_gen_planes_refined0.006
r_bond_refined_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4665
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction