8JBS

B12-binding domain from Chloracidobacterium thermophilum MerR family protein, dark state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.1M Amino acids, 0.1 M Buffer System 3 (Bicine and Tris) pH 8.5, 50% v/v Precipitant Mix 3 (Glycerol and Poly(ethylene glycol) 4000)
Crystal Properties
Matthews coefficientSolvent content
2.2946.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.218α = 90
b = 125.218β = 90
c = 73.088γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9762DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim 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
12.3108.4421000.163112.520.629650
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)
12.32.3498.912.6590.5380.6219.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.3108.4428126150399.920.187910.185310.23609RANDOM59.044
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]
-2.25-1.12-2.257.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.45
r_long_range_B_other9.876
r_long_range_B_refined9.874
r_dihedral_angle_2_deg9.541
r_scangle_other8.293
r_mcangle_it6.933
r_mcangle_other6.933
r_dihedral_angle_1_deg6.659
r_scbond_it5.79
r_scbond_other5.789
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.45
r_long_range_B_other9.876
r_long_range_B_refined9.874
r_dihedral_angle_2_deg9.541
r_scangle_other8.293
r_mcangle_it6.933
r_mcangle_other6.933
r_dihedral_angle_1_deg6.659
r_scbond_it5.79
r_scbond_other5.789
r_mcbond_it5.055
r_mcbond_other5.044
r_angle_refined_deg2.021
r_angle_other_deg0.609
r_chiral_restr0.092
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3788
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing