8E7R

Crystal Structure of FosB from Bacillus cereus with Zinc and Phosphonoacetate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529816% PEG 3350, 125 mM magnesium formate, 5 mM phosphonoacetate
Crystal Properties
Matthews coefficientSolvent content
2.3246.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.674α = 90
b = 67.831β = 90
c = 69.738γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2022-06-15MSINGLE 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)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
11.9755099.80.160.1780.0773.65.222012
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)
11.982.0199.80.5830.6520.2870.7525

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 REPLACEMENTTHROUGHOUT4JH61.97546.80821965104999.2230.1720.16910.2204RANDOM17.79
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.881
r_dihedral_angle_3_deg13.531
r_dihedral_angle_2_deg7.656
r_dihedral_angle_1_deg6.97
r_lrange_it4.779
r_lrange_other4.673
r_scangle_it3.113
r_scangle_other3.113
r_scbond_it1.97
r_scbond_other1.956
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.881
r_dihedral_angle_3_deg13.531
r_dihedral_angle_2_deg7.656
r_dihedral_angle_1_deg6.97
r_lrange_it4.779
r_lrange_other4.673
r_scangle_it3.113
r_scangle_other3.113
r_scbond_it1.97
r_scbond_other1.956
r_mcangle_it1.928
r_mcangle_other1.927
r_angle_refined_deg1.444
r_mcbond_it1.296
r_mcbond_other1.295
r_angle_other_deg0.779
r_nbd_refined0.22
r_symmetry_nbd_other0.21
r_nbd_other0.196
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.155
r_symmetry_nbd_refined0.149
r_symmetry_xyhbond_nbd_refined0.131
r_symmetry_nbtor_other0.084
r_metal_ion_refined0.079
r_chiral_restr0.073
r_gen_planes_other0.01
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2326
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms35

Software

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