9FCT

BtuJ1 - Bacteroides thetaiotaomicron B12 scavenging protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.529329% w/v PEG, 0.2M sodium citrate pH 3.5
Crystal Properties
Matthews coefficientSolvent content
2.6954.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.891α = 90
b = 51.416β = 131.789
c = 108.757γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2024-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.873ESRFID23-2

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
11.681.09820.20.20.10.9681.74.46625813.12
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.70.381

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.60381.0966257342982.0480.190.18860.213220.543
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]
0.1280.159-1.0480.245
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.039
r_dihedral_angle_3_deg11.096
r_dihedral_angle_2_deg9.459
r_dihedral_angle_1_deg8.647
r_lrange_it7.503
r_lrange_other6.593
r_angle_refined_deg2.351
r_scangle_it2.295
r_scangle_other2.294
r_mcangle_it2.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.039
r_dihedral_angle_3_deg11.096
r_dihedral_angle_2_deg9.459
r_dihedral_angle_1_deg8.647
r_lrange_it7.503
r_lrange_other6.593
r_angle_refined_deg2.351
r_scangle_it2.295
r_scangle_other2.294
r_mcangle_it2.044
r_mcangle_other2.044
r_angle_other_deg1.401
r_scbond_it1.388
r_scbond_other1.388
r_mcbond_it1.172
r_mcbond_other1.172
r_nbtor_refined0.149
r_nbd_refined0.142
r_symmetry_nbd_other0.115
r_chiral_restr0.111
r_nbd_other0.111
r_symmetry_xyhbond_nbd_refined0.1
r_symmetry_nbd_refined0.083
r_xyhbond_nbd_refined0.08
r_ncsr_local_group_10.066
r_symmetry_nbtor_other0.059
r_bond_refined_d0.014
r_gen_planes_refined0.013
r_gen_planes_other0.01
r_bond_other_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3674
Nucleic Acid Atoms
Solvent Atoms497
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing