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Structural analysis of DegS, a stress sensor of the bacterial periplasm
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other DegP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.05 M MgCl2, 0.1 M Hepes, pH 7.5, 30% Polyethylene Glycol Monomethyl ether 550, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.7 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.28 α = 90 b = 166.28 β = 90 c = 166.28 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 CCD ADSC QUANTUM 4 mirrors 2004-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 2.2 32 98.6 0.048 5.4 38296 3
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 2.2 98.6 0.39 3 5.4 38296
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 DegP 2.2 32.62 36364 1927 99.05 0.24711 0.24459 0.2426 0.29526 0.2918 RANDOM 55.471
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 11.653 r_scangle_it 5.636 r_scbond_it 3.897 r_mcangle_it 2.635 r_angle_refined_deg 2.413 r_mcbond_it 1.605 r_symmetry_hbond_refined 0.397 r_symmetry_vdw_refined 0.366 r_chiral_restr 0.35 r_nbd_refined 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 11.653 r_scangle_it 5.636 r_scbond_it 3.897 r_mcangle_it 2.635 r_angle_refined_deg 2.413 r_mcbond_it 1.605 r_symmetry_hbond_refined 0.397 r_symmetry_vdw_refined 0.366 r_chiral_restr 0.35 r_nbd_refined 0.349 r_xyhbond_nbd_refined 0.264 r_bond_refined_d 0.025 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4666 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing