7E6F

Crystal structure of PMP-bound form of cysteine desulfurase SufS R376A from Bacillus subtilis in L-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
3.4664.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.8α = 90
b = 92.8β = 90
c = 129.5γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.000Photon FactoryBL-17A

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
12.7446.4499.90.110.1130.99819.7420.2251747175.225
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)
12.742.841000.9210.9450.9184.3920.068

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 REPLACEMENTTHROUGHOUT5ZS92.7446.441659787499.950.16690.16450.2125RANDOM75.465
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]
0.10.050.1-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.455
r_dihedral_angle_4_deg19.829
r_dihedral_angle_3_deg17.401
r_dihedral_angle_1_deg6.598
r_angle_refined_deg2.055
r_chiral_restr0.137
r_bond_refined_d0.011
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3199
Nucleic Acid Atoms
Solvent Atoms8
Heterogen Atoms27

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing