4F64

Crystal structure of Human Fibroblast Growth Factor Receptor 1 Kinase domain in complex with compound 6


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
2.6553.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.81α = 90
b = 57.277β = 107.55
c = 65.433γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRIGAKU SATURN 922004-12-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.0561.93196.750.1490.1286.62.7465554483911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1696.060.5720.5042.22.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1FGK2.0561.94483942144224895.360.217010.214260.26912RANDOM26.505
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]
-2.11-0.963.77-2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.054
r_dihedral_angle_4_deg15.722
r_dihedral_angle_3_deg14.372
r_dihedral_angle_1_deg5.795
r_scangle_it3.149
r_scbond_it2.45
r_angle_refined_deg1.403
r_mcangle_it1.245
r_mcbond_it0.915
r_angle_other_deg0.831
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.054
r_dihedral_angle_4_deg15.722
r_dihedral_angle_3_deg14.372
r_dihedral_angle_1_deg5.795
r_scangle_it3.149
r_scbond_it2.45
r_angle_refined_deg1.403
r_mcangle_it1.245
r_mcbond_it0.915
r_angle_other_deg0.831
r_mcbond_other0.459
r_symmetry_vdw_other0.293
r_nbd_refined0.204
r_nbd_other0.194
r_nbtor_refined0.176
r_xyhbond_nbd_refined0.159
r_symmetry_hbond_refined0.145
r_chiral_restr0.087
r_nbtor_other0.084
r_symmetry_vdw_refined0.082
r_bond_refined_d0.014
r_bond_other_d0.006
r_gen_planes_refined0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4229
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms73

Software

Software
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling