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Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated
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 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.96 α = 90 b = 43.96 β = 90 c = 52.329 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 IMAGE PLATE RIGAKU RAXIS IV++ 2012-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.
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 1.617 52.31 97.4 0.03 34.4 5.1 14075
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 1.617 1.623 70 0.18 5.9 3.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIR THROUGHOUT 1.617 38.07 12805 686 93.32 0.205 0.20333 0.1961 0.23572 0.2299 RANDOM 18.652
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] 0.4 0.4 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.763 r_dihedral_angle_4_deg 13.44 r_dihedral_angle_3_deg 13.329 r_long_range_B_refined 5.988 r_dihedral_angle_1_deg 5.479 r_mcangle_it 1.74 r_scbond_it 1.575 r_angle_refined_deg 1.349 r_mcbond_it 1.041 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.763 r_dihedral_angle_4_deg 13.44 r_dihedral_angle_3_deg 13.329 r_long_range_B_refined 5.988 r_dihedral_angle_1_deg 5.479 r_mcangle_it 1.74 r_scbond_it 1.575 r_angle_refined_deg 1.349 r_mcbond_it 1.041 r_chiral_restr 0.097 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 798 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling autoSHARP phasing