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Crystal structure of FGFR4 kinase domain in complex with covalent inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 277 100 mM Bis-Tris pH 5.5, 14% (w/v) polyethylene glycol 3,350, 200 mM lithium sulfate and 2% (w/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.3 46.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.067 α = 90 b = 58.67 β = 97.57 c = 60.747 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 CCD OXFORD SAPPHIRE CCD 2013-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0000 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.9 42.02 98.6 0.049 13.2 3.3 24253 32.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.99 0.56
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3OXZ 1.9 42.02 24186 1231 99.1 0.201 0.199 0.1989 0.227 0.2299 RANDOM 37.4
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] -0.0989 -1.187 -0.5259 0.6247
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.92 t_omega_torsion 3.13 t_angle_deg 0.96 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.92 t_omega_torsion 3.13 t_angle_deg 0.96 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2210 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 45
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing