7E6B

Crystal structure of PMP-bound form of cysteine desulfurase SufS C361A from Bacillus subtilis


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
3.4464.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.8α = 90
b = 92.8β = 90
c = 129γ = 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
11.8446.441000.0660.068124.3519.615630642.667
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)
11.841.941000.7130.7310.9384.3520.874

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 REPLACEMENTTHROUGHOUT5ZS91.8446.4453490281699.990.15840.15730.1784RANDOM42.234
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]
0.030.010.03-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.921
r_dihedral_angle_4_deg18.943
r_dihedral_angle_3_deg14.89
r_dihedral_angle_1_deg6.502
r_angle_refined_deg2.457
r_chiral_restr0.198
r_bond_refined_d0.021
r_gen_planes_refined0.016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3195
Nucleic Acid Atoms
Solvent Atoms214
Heterogen Atoms90

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing