4D8T

Crystal structure of D-Cysteine desulfhydrase from Salmonella typhimurium at 2.2 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.62981.5M Ammonium sulphate, 15% (v/v) ethylene glycol, 0.1M HEPES, 0.2% Benzamidine, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.483α = 90
b = 165.45β = 119.01
c = 69.208γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2009-11-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.2160.4598.40.06911.83.36389223.53
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)
12.212.33900.2015.13.18500

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1J0B2.2829.1954711292697.590.191370.188690.24182RANDOM33.526
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]
-0.01-0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.355
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg13.892
r_dihedral_angle_1_deg5.536
r_angle_refined_deg1.171
r_chiral_restr0.076
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.355
r_dihedral_angle_4_deg15.638
r_dihedral_angle_3_deg13.892
r_dihedral_angle_1_deg5.536
r_angle_refined_deg1.171
r_chiral_restr0.076
r_bond_refined_d0.006
r_gen_planes_refined0.005
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9678
Nucleic Acid Atoms
Solvent Atoms450
Heterogen Atoms66

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling