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Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BKD PDB ENTRY 1BKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 1.2-1.5 M phosphate, 100 mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.77 67.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.312 α = 90 b = 183.312 β = 90 c = 178.509 γ = 90
Symmetry Space Group I 4 2 2
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 SBC-2 mirrors 2001-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 43 99.4 0.11 18.7 10 75882 75882 -3 32.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 99.9 0.512 3.3 10.1 7541
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 1BKD 2.2 43.21 73293 73293 4399 95.7 0.186 0.186 0.186 0.186 0.211 0.2106 RANDOM 35.7
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] 1.59 1.59 -3.17
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.7 c_scangle_it 4.07 c_scbond_it 2.82 c_mcangle_it 2.45 c_angle_deg 1.5 c_mcbond_it 1.49 c_improper_angle_d 0.97 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6540 Nucleic Acid Atoms Solvent Atoms 514 Heterogen Atoms 58
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing