4F63

Crystal structure of Human Fibroblast Growth Factor Receptor 1 Kinase domain in complex with compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FGKPDB ENTRY 1FGK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27716-20% PEG8000, 100 mM PCTP, 100-300 mM ammonium sulfate, 25% ethylene glycol, pH 6.25-7.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6653.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.306α = 90
b = 57.477β = 107.42
c = 65.452γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRIGAKU SATURN 922004-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54179

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
12.5517.3397.030.0938.762.63243142365211
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)
12.552.6997.840.711.822.59

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1FGK2.5517.3322438121497.280.232230.22930.28741RANDOM35.576
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]
-1.71-0.983.56-2.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.489
r_dihedral_angle_4_deg15.581
r_dihedral_angle_3_deg14.958
r_dihedral_angle_1_deg6.13
r_scangle_it2.744
r_scbond_it2.39
r_angle_refined_deg1.421
r_mcangle_it0.964
r_angle_other_deg0.812
r_mcbond_it0.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.489
r_dihedral_angle_4_deg15.581
r_dihedral_angle_3_deg14.958
r_dihedral_angle_1_deg6.13
r_scangle_it2.744
r_scbond_it2.39
r_angle_refined_deg1.421
r_mcangle_it0.964
r_angle_other_deg0.812
r_mcbond_it0.767
r_mcbond_other0.592
r_nbd_refined0.226
r_symmetry_vdw_other0.208
r_nbd_other0.194
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.177
r_symmetry_hbond_refined0.126
r_symmetry_vdw_refined0.094
r_nbtor_other0.086
r_chiral_restr0.072
r_xyhbond_nbd_other0.031
r_bond_refined_d0.013
r_bond_other_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4229
Nucleic Acid Atoms
Solvent Atoms28
Heterogen Atoms62

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling