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Crystal structure of FGFR4 domain 3 in complex with a de novo-designed mini-binder in P21 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 0.1 M Bis-Tris (pH 5.5)
25% polyethylene glycol 3,350
3% 1,5-diaminopentane dihydrochloride
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.798 α = 90 b = 58.664 β = 110.926 c = 68.055 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2021-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.85 50 96.1 0.992 18.55 4.9 8780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 87.3 0.889 2.564 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1CVS 2.86 49.32 1.41 8733 443 95.53 0.2704 0.2684 0.2697 0.3063 0.3002 58.09
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.2565 f_angle_d 0.5457 f_chiral_restr 0.0391 f_plane_restr 0.003 f_bond_d 0.0027
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2164 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing