5U6F

Bacterial adhesin from Mobiluncus mulieris containing intramolecular disulfide, isopeptide, and ester bond cross-links (space group P21)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529110% (v/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate), and 0.1 M MES/Imidazole (pH 6.5).
Crystal Properties
Matthews coefficientSolvent content
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.548α = 90
b = 51.604β = 101.6
c = 81.206γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.579.54797.1122.37.443553
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)
11.51.5395.50.9192.77

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 REPLACEMENTTHROUGHOUTin-house SAD model1.579.5541295221796.780.235460.233830.26653RANDOM19.294
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]
-3.02-1.262.960.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.997
r_dihedral_angle_3_deg11.997
r_dihedral_angle_4_deg9.119
r_dihedral_angle_1_deg6.288
r_long_range_B_refined2.84
r_long_range_B_other2.803
r_scangle_other1.847
r_mcangle_it1.325
r_mcangle_other1.324
r_angle_refined_deg1.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.997
r_dihedral_angle_3_deg11.997
r_dihedral_angle_4_deg9.119
r_dihedral_angle_1_deg6.288
r_long_range_B_refined2.84
r_long_range_B_other2.803
r_scangle_other1.847
r_mcangle_it1.325
r_mcangle_other1.324
r_angle_refined_deg1.288
r_scbond_it1.149
r_scbond_other1.149
r_angle_other_deg0.817
r_mcbond_it0.816
r_mcbond_other0.814
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms2152
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing