5HBO

Native rhodanese domain of YgaP prepared without DDT is both S-nitrosylated and S-sulfhydrated


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HBL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52950.2 M sodium acetate in 0.1 M Tris HCl pH 8.5, and 30% PEG 4000.
Crystal Properties
Matthews coefficientSolvent content
2.0640.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.683α = 90
b = 43.683β = 90
c = 52.417γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-21.127SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6637.898.628.15.413034
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.7591.30.1976.64.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5HBL1.6637.81237864398.560.176630.175560.19858RANDOM17.659
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]
-0.14-0.07-0.140.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.008
r_dihedral_angle_4_deg13.688
r_dihedral_angle_3_deg12.616
r_long_range_B_refined5.57
r_long_range_B_other5.109
r_dihedral_angle_1_deg4.922
r_scangle_other1.546
r_mcangle_it1.366
r_mcangle_other1.365
r_angle_refined_deg1.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.008
r_dihedral_angle_4_deg13.688
r_dihedral_angle_3_deg12.616
r_long_range_B_refined5.57
r_long_range_B_other5.109
r_dihedral_angle_1_deg4.922
r_scangle_other1.546
r_mcangle_it1.366
r_mcangle_other1.365
r_angle_refined_deg1.323
r_angle_other_deg0.981
r_scbond_it0.945
r_scbond_other0.944
r_mcbond_it0.787
r_mcbond_other0.783
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms787
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing