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Ras guanine nucleotide exchange factor SOS2 (Rem-cdc25), with surface mutations
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Protein 10.3 mg/ml in 25 mM Tris HCl, pH 7.5, 100 mM NaCl, 1 mM DTT. Reservoir 0,1 M Natriumacetat, 20% w/v PEG 3350. Cryo buffer was reservoir supplemented with 15% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.33 47.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.97 α = 90 b = 53.97 β = 90 c = 183.793 γ = 90
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 PILATUS 6M-F 2016-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.0332 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.72 46.54 96.9 0.067 0.998 14.1 4.8 13644 69.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.72 2.88 82.7 0.539 0.761 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1NVU 2.72 46.54 12960 683 96.94 0.22171 0.21836 0.28526 0.2684 RANDOM 79.654
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] -6.06 -6.06 12.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.999 r_dihedral_angle_3_deg 17.663 r_dihedral_angle_4_deg 15.263 r_long_range_B_refined 7.026 r_long_range_B_other 7.026 r_dihedral_angle_1_deg 6.278 r_mcangle_it 4.737 r_mcangle_other 4.736 r_scangle_other 4.562 r_mcbond_other 2.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.999 r_dihedral_angle_3_deg 17.663 r_dihedral_angle_4_deg 15.263 r_long_range_B_refined 7.026 r_long_range_B_other 7.026 r_dihedral_angle_1_deg 6.278 r_mcangle_it 4.737 r_mcangle_other 4.736 r_scangle_other 4.562 r_mcbond_other 2.793 r_mcbond_it 2.792 r_scbond_it 2.554 r_scbond_other 2.553 r_angle_refined_deg 1.244 r_angle_other_deg 0.951 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3793 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing