7POO

Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis in complex with foliosidine in P212121.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P24 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1525 % (w/v) PEG 3350 0.2 M ammonium acetate 0.1M Bis Tris pH 5.5 Cryoprotection by soaking for 15-30 seconds in mother liquor supplemented with 2.5M L-proline.
Crystal Properties
Matthews coefficientSolvent content
2.5251.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.55α = 90
b = 83.06β = 90
c = 157.48γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.7157.598.10.1840.999.85.725344
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.730.9620.73

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 REPLACEMENTTHROUGHOUT3p242.773.472531770698.20.21630.21550.2425RANDOM68.02
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]
-4.47720.0837-15.6066
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.11
t_other_torsion3.03
t_angle_deg0.92
t_bond_d0.009
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.11
t_other_torsion3.03
t_angle_deg0.92
t_bond_d0.009
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5499
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms78

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing