7E6E

Crystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in D-cycloserine-inhibition


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5ZS9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M Tris-HCl, 50 mM Lithium sulfate, 50%(v/v) PEG200
Crystal Properties
Matthews coefficientSolvent content
3.4163.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.4α = 90
b = 92.4β = 90
c = 128.7γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
12.2846.241000.0660.068129.9719.7212958358.813
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.381000.9160.940.9013.6820.092

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 REPLACEMENTTHROUGHOUT5ZS92.2846.2428103147999.980.16280.1620.1782RANDOM58.486
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]
0.150.080.15-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.561
r_dihedral_angle_4_deg20.757
r_dihedral_angle_3_deg16.894
r_dihedral_angle_1_deg6.745
r_angle_refined_deg1.962
r_chiral_restr0.131
r_bond_refined_d0.013
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3209
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms81

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing