8Q4K

Crystal structure of Borrelia burgdorferi BB0158


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62940.2 M ammonium sulfate 0.1 M sodium acetate (pH 4.6) 20% PEG 2000 MME
Crystal Properties
Matthews coefficientSolvent content
2.4249.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.063α = 90
b = 81.774β = 109.381
c = 80.801γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2022-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918400BESSY14.1

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
12.444.9799.30.0740.998156.935959
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)
12.42.490.4030.9384

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 REPLACEMENTTHROUGHOUT2.444.9735949182199.2550.2170.2130.297348.838
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]
-0.0020.004-0.0030.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.938
r_dihedral_angle_3_deg17.399
r_lrange_it9.115
r_lrange_other9.109
r_dihedral_angle_1_deg7.818
r_scangle_it6.417
r_scangle_other6.417
r_mcangle_it6.044
r_mcangle_other6.044
r_scbond_it4.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.938
r_dihedral_angle_3_deg17.399
r_lrange_it9.115
r_lrange_other9.109
r_dihedral_angle_1_deg7.818
r_scangle_it6.417
r_scangle_other6.417
r_mcangle_it6.044
r_mcangle_other6.044
r_scbond_it4.24
r_scbond_other4.206
r_mcbond_it4.115
r_mcbond_other4.113
r_angle_other_deg2.287
r_angle_refined_deg1.567
r_symmetry_nbd_refined0.343
r_nbd_other0.303
r_symmetry_nbd_other0.222
r_nbd_refined0.21
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_refined0.103
r_symmetry_nbtor_other0.072
r_chiral_restr0.065
r_symmetry_xyhbond_nbd_other0.064
r_bond_other_d0.034
r_bond_refined_d0.008
r_gen_planes_other0.008
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6473
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing