8DVH

Crystal structure of ATP-dependent Lon protease from Bacillus subtillis (BsLonBA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RRE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.829835% PEG400 at pH 7.8
Crystal Properties
Matthews coefficientSolvent content
2.2545.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.892α = 90
b = 89.892β = 90
c = 83.95γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-ID

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
11.98499.90.04430.19.729405739.59
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.940.827

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 REPLACEMENTTHROUGHOUT1rre1.977.852945195199.910.19540.19390.2371RANDOM43.785
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]
-1.36-0.68-1.364.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.72
r_dihedral_angle_4_deg15.808
r_dihedral_angle_3_deg14.933
r_dihedral_angle_1_deg7.095
r_angle_refined_deg1.687
r_angle_other_deg1.351
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.72
r_dihedral_angle_4_deg15.808
r_dihedral_angle_3_deg14.933
r_dihedral_angle_1_deg7.095
r_angle_refined_deg1.687
r_angle_other_deg1.351
r_chiral_restr0.071
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2831
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms58

Software

Software
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
PHENIXmodel building
PHASERphasing
Aimlessdata scaling
XDSdata reduction