8G7F

Crystal Structure of FosB from Bacillus cereus with Zinc and 1-hydroxypropylphosphonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JH6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298Protein solution (10 mg/mL FosB in 20 mM HEPES buffer, pH 7.5 and 5 mM inhibitor) and reservoir solution (125 mM Mg formate and 20% (w/v) poly(ethylene glycol) (PEG) 3350) were mixed in a Hampton Research VDX plate with a 1:1 ratio of the solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen
Crystal Properties
Matthews coefficientSolvent content
2.346.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.2α = 90
b = 68.273β = 90
c = 69.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-09-26MSINGLE 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
12.045099.90.9693.33.920106
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)
12.042.081000.73.9

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 REPLACEMENTTHROUGHOUT4JH62.0447.2719077102899.890.163950.161360.21492RANDOM20.595
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]
0.04-0.02-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.919
r_dihedral_angle_4_deg16.644
r_dihedral_angle_3_deg12.354
r_dihedral_angle_1_deg7.491
r_long_range_B_refined4.894
r_long_range_B_other4.792
r_scangle_other3.412
r_angle_other_deg2.261
r_scbond_it2.12
r_scbond_other2.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.919
r_dihedral_angle_4_deg16.644
r_dihedral_angle_3_deg12.354
r_dihedral_angle_1_deg7.491
r_long_range_B_refined4.894
r_long_range_B_other4.792
r_scangle_other3.412
r_angle_other_deg2.261
r_scbond_it2.12
r_scbond_other2.104
r_mcangle_it2.046
r_mcangle_other2.045
r_angle_refined_deg1.483
r_mcbond_it1.371
r_mcbond_other1.37
r_chiral_restr0.073
r_bond_other_d0.034
r_gen_planes_other0.011
r_bond_refined_d0.009
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2324
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction