8G7G

Crystal Structure of FosB from Bacillus cereus with Zinc and (1-hydroxy-2-methylpropyl)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 (50 mM Mg formate and 16% (w/v) PEG 3350) were mixed in a Hampton Research VDX plate with a 1:1 ratio of each solution. Cryoprotected in its reservoir solution with 20% glycerol added prior to rapid freezing in liquid nitrogen.
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.234α = 90
b = 68.534β = 90
c = 69.541γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-06-15MSINGLE 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
12.235099.70.1440.1540.0550.9864.27.815452
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)
12.232.2798.50.5520.60.2260.8456.6

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 REPLACEMENTTHROUGHOUT4JH62.2347.1851540575699.0480.1810.17730.2461RANDOM22.768
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]
-0.0030.004-0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.163
r_dihedral_angle_3_deg14.2
r_dihedral_angle_1_deg7.591
r_lrange_it5.193
r_lrange_other5.178
r_scangle_it3.618
r_scangle_other3.617
r_mcangle_it2.373
r_mcangle_other2.372
r_scbond_it2.201
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg17.163
r_dihedral_angle_3_deg14.2
r_dihedral_angle_1_deg7.591
r_lrange_it5.193
r_lrange_other5.178
r_scangle_it3.618
r_scangle_other3.617
r_mcangle_it2.373
r_mcangle_other2.372
r_scbond_it2.201
r_scbond_other2.189
r_mcbond_it1.534
r_mcbond_other1.534
r_angle_refined_deg1.514
r_dihedral_angle_2_deg1.126
r_angle_other_deg0.813
r_symmetry_nbd_other0.209
r_nbd_refined0.195
r_nbd_other0.184
r_nbtor_refined0.17
r_xyhbond_nbd_refined0.161
r_symmetry_xyhbond_nbd_refined0.141
r_metal_ion_refined0.087
r_symmetry_nbd_refined0.085
r_symmetry_xyhbond_nbd_other0.076
r_symmetry_nbtor_other0.075
r_chiral_restr0.07
r_bond_refined_d0.014
r_gen_planes_other0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2324
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms25

Software

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