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Crystal structure of Human Fibroblast Growth Factor Receptor 1 Kinase domain in complex with compound 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FGK PDB ENTRY 1FGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 16-20% 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 coefficient Solvent content 2.66 53.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 208.306 α = 90 b = 57.477 β = 107.42 c = 65.452 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD RIGAKU SATURN 92 2004-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54179
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 2.55 17.33 97.03 0.093 8.76 2.63 24314 23652 1 1
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 2.55 2.69 97.84 0.71 1.82 2.59
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 PDB ENTRY 1FGK 2.55 17.33 22438 1214 97.28 0.23223 0.2293 0.236 0.28741 0.2846 RANDOM 35.576
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 -0.98 3.56 -2.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.489 r_dihedral_angle_4_deg 15.581 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 6.13 r_scangle_it 2.744 r_scbond_it 2.39 r_angle_refined_deg 1.421 r_mcangle_it 0.964 r_angle_other_deg 0.812 r_mcbond_it 0.767
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.489 r_dihedral_angle_4_deg 15.581 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 6.13 r_scangle_it 2.744 r_scbond_it 2.39 r_angle_refined_deg 1.421 r_mcangle_it 0.964 r_angle_other_deg 0.812 r_mcbond_it 0.767 r_mcbond_other 0.592 r_nbd_refined 0.226 r_symmetry_vdw_other 0.208 r_nbd_other 0.194 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.126 r_symmetry_vdw_refined 0.094 r_nbtor_other 0.086 r_chiral_restr 0.072 r_xyhbond_nbd_other 0.031 r_bond_refined_d 0.013 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4229 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 62
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling