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Acidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AXM PDB ENTRY 1AXM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 295 Crystals of thecomplex between FGF-1 and 2,5-DHPS (2,5-dihydroxyphenylsulfonate) were grown using the sitting drop vapour method at 295 K. Equal volumes of protein and inhibitor solutions, 0.75 and 1.5mM, respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5mM sodium phosphate [pH 7.8]. The drops were equilibrated against 0.2ml of 1.3M Li2SO4 and typical crystals grew within two weeks with approximate dimensions of 0.7 x 0.5 x 0.2 mm.
, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.44 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.022 α = 90 b = 47.349 β = 106.64 c = 97.975 γ = 90
Symmetry Space Group P 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 100 CCD ADSC QUANTUM 210r 2008-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 0.979 ESRF BM16
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 1.98 94.07 98.6 0.05 16 3.7 59910 59016 29.604
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) 1.98 2.09 92.8 0.342 4.5 3.3 8011
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1AXM 1.98 24.48 59016 56030 2981 98.5 0.232 0.23041 0.22718 0.2283 0.28958 0.2888 RANDOM 36.077
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] 0.73 0.61 1.01 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_4_deg 19.25 r_dihedral_angle_3_deg 18.798 r_dihedral_angle_1_deg 8.245 r_scangle_it 5.07 r_scbond_it 3.596 r_mcangle_it 2.713 r_angle_refined_deg 2.273 r_mcbond_it 1.669 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_4_deg 19.25 r_dihedral_angle_3_deg 18.798 r_dihedral_angle_1_deg 8.245 r_scangle_it 5.07 r_scbond_it 3.596 r_mcangle_it 2.713 r_angle_refined_deg 2.273 r_mcbond_it 1.669 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.265 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.187 r_chiral_restr 0.161 r_symmetry_hbond_refined 0.154 r_bond_refined_d 0.026 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6228 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 24
Software Software Software Name Purpose DNA data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling