8G7H

Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxypropan-2-yl)phosphonic 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 (75 mM Mg formate and 14% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate using a 2:3 ratio of protein:reservoir solutions. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen
Crystal Properties
Matthews coefficientSolvent content
2.2946.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.233α = 90
b = 68.21β = 90
c = 69.826γ = 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)Rrim I (All)Rpim 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
11.815099.90.1380.1450.0440.9944.110.728683
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.841000.7850.8290.2630.8419.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4JH61.8148.79328626146299.7250.1560.15430.1852RANDOM19.454
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]
0.002-0.0040.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.519
r_dihedral_angle_3_deg13.282
r_dihedral_angle_1_deg6.897
r_lrange_it6.454
r_lrange_other6.342
r_dihedral_angle_2_deg5.582
r_scangle_it4.495
r_scangle_other4.493
r_scbond_it2.835
r_scbond_other2.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.519
r_dihedral_angle_3_deg13.282
r_dihedral_angle_1_deg6.897
r_lrange_it6.454
r_lrange_other6.342
r_dihedral_angle_2_deg5.582
r_scangle_it4.495
r_scangle_other4.493
r_scbond_it2.835
r_scbond_other2.834
r_mcangle_it2.187
r_mcangle_other2.187
r_mcbond_it1.603
r_mcbond_other1.602
r_angle_refined_deg1.52
r_angle_other_deg0.832
r_nbd_refined0.231
r_symmetry_nbd_refined0.212
r_symmetry_nbd_other0.21
r_nbd_other0.207
r_nbtor_refined0.193
r_symmetry_xyhbond_nbd_other0.19
r_xyhbond_nbd_refined0.163
r_symmetry_xyhbond_nbd_refined0.158
r_metal_ion_refined0.115
r_symmetry_nbtor_other0.084
r_chiral_restr0.079
r_gen_planes_other0.012
r_gen_planes_refined0.009
r_bond_refined_d0.008
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2324
Nucleic Acid Atoms
Solvent Atoms270
Heterogen Atoms47

Software

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