9CD5

FGFR1 Kinase Domain Soak with Inhibitor TYRA-300


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherFGFR1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.527725%P8K, 25% EG, 0.25M AS, 0.1MPCTP pH7.5
Crystal Properties
Matthews coefficientSolvent content
2.6553.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 206.03α = 90
b = 57.614β = 107.185
c = 65.694γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCD2020-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54184

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
12.93949.25699.80.1410.160.0740.9887.94.515930
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)
12.9393.0498.40.630.7820.4540.6861.42.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE2.93949.2561592477399.7240.2150.2130.262946.308
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]
-0.44-0.9142.168-0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.953
r_dihedral_angle_3_deg12.433
r_dihedral_angle_2_deg12.425
r_lrange_it7.287
r_lrange_other7.155
r_dihedral_angle_1_deg5.65
r_scangle_it2.609
r_scangle_other2.265
r_mcangle_it1.895
r_mcangle_other1.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg12.953
r_dihedral_angle_3_deg12.433
r_dihedral_angle_2_deg12.425
r_lrange_it7.287
r_lrange_other7.155
r_dihedral_angle_1_deg5.65
r_scangle_it2.609
r_scangle_other2.265
r_mcangle_it1.895
r_mcangle_other1.895
r_scbond_it1.571
r_scbond_other1.333
r_mcbond_it1.072
r_mcbond_other1.072
r_angle_refined_deg0.914
r_angle_other_deg0.335
r_nbd_refined0.196
r_symmetry_nbd_other0.175
r_nbtor_refined0.172
r_symmetry_xyhbond_nbd_refined0.166
r_nbd_other0.145
r_xyhbond_nbd_refined0.137
r_symmetry_nbd_refined0.1
r_ncsr_local_group_10.087
r_symmetry_xyhbond_nbd_other0.075
r_symmetry_nbtor_other0.073
r_chiral_restr0.043
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4539
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms151

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata scaling
SAINTdata reduction
PHASERphasing