7OZY

FGFR2 kinase domain (residues 461-763) in complex with 38.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PVF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.629125% w/v PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
2.7354.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.839α = 90
b = 113.839β = 90
c = 117.408γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2017-11-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

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
12.2880.5499.90.1410.1520.0560.9896.67.135802
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)
12.282.342.5882.7771.3890.683

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2PVF2.2880.535216169198.30.2430.24030.295950.923
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]
-1.096-1.0962.192
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.054
r_dihedral_angle_4_deg18.383
r_dihedral_angle_3_deg14.416
r_lrange_other8.089
r_lrange_it8.088
r_dihedral_angle_1_deg7.188
r_scangle_it5.715
r_scangle_other5.714
r_mcangle_it5.565
r_mcangle_other5.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.054
r_dihedral_angle_4_deg18.383
r_dihedral_angle_3_deg14.416
r_lrange_other8.089
r_lrange_it8.088
r_dihedral_angle_1_deg7.188
r_scangle_it5.715
r_scangle_other5.714
r_mcangle_it5.565
r_mcangle_other5.564
r_scbond_it3.686
r_scbond_other3.686
r_mcbond_it3.675
r_mcbond_other3.671
r_angle_refined_deg1.43
r_angle_other_deg1.186
r_symmetry_nbd_refined0.267
r_nbd_other0.194
r_nbd_refined0.188
r_symmetry_nbd_other0.177
r_symmetry_xyhbond_nbd_refined0.164
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.158
r_symmetry_nbtor_other0.076
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_symmetry_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4389
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms70

Software

Software
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement