☰ Navigation Tabs
Native rhodanese domain of YgaP prepared without DDT is both S-nitrosylated and S-sulfhydrated
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 0.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.06 40.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.683 α = 90 b = 43.683 β = 90 c = 52.417 γ = 120
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 315r 2013-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.127 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.66 37.8 98.6 28.1 5.4 13034
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 1.66 1.75 91.3 0.197 6.6 4.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5HBL 1.66 37.8 12378 643 98.56 0.17663 0.17556 0.1867 0.19858 0.2026 RANDOM 17.659
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] -0.14 -0.07 -0.14 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.008 r_dihedral_angle_4_deg 13.688 r_dihedral_angle_3_deg 12.616 r_long_range_B_refined 5.57 r_long_range_B_other 5.109 r_dihedral_angle_1_deg 4.922 r_scangle_other 1.546 r_mcangle_it 1.366 r_mcangle_other 1.365 r_angle_refined_deg 1.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.008 r_dihedral_angle_4_deg 13.688 r_dihedral_angle_3_deg 12.616 r_long_range_B_refined 5.57 r_long_range_B_other 5.109 r_dihedral_angle_1_deg 4.922 r_scangle_other 1.546 r_mcangle_it 1.366 r_mcangle_other 1.365 r_angle_refined_deg 1.323 r_angle_other_deg 0.981 r_scbond_it 0.945 r_scbond_other 0.944 r_mcbond_it 0.787 r_mcbond_other 0.783 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 787 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing