6PI5

The evolving story of AtzT, a periplasmic binding protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293Protein at 20 mg/mL in SD2 plates incubated at 20 C. Crystallisation conditions contained 6-8% Jeffamine M600 with 2-7% MPD and trisodium citrate at 1.1-1.2 M
Crystal Properties
Matthews coefficientSolvent content
2.4549.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.006α = 90
b = 63.142β = 93.55
c = 120.373γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.953723Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.6749.399.30.0830.0340.99811.96.8171863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.671.793.20.6430.2850.7692.75.8

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 REPLACEMENTTHROUGHOUT6PII1.6749.3163254858199.270.15750.156110.18414RANDOM24.432
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]
-0.540.22-0.170.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.349
r_dihedral_angle_3_deg14.157
r_dihedral_angle_4_deg8.779
r_long_range_B_refined6.437
r_long_range_B_other6.437
r_scangle_other5.934
r_dihedral_angle_1_deg5.762
r_scbond_it3.886
r_scbond_other3.886
r_mcangle_it3.142
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.349
r_dihedral_angle_3_deg14.157
r_dihedral_angle_4_deg8.779
r_long_range_B_refined6.437
r_long_range_B_other6.437
r_scangle_other5.934
r_dihedral_angle_1_deg5.762
r_scbond_it3.886
r_scbond_other3.886
r_mcangle_it3.142
r_mcangle_other3.142
r_mcbond_it2.249
r_mcbond_other2.249
r_angle_refined_deg1.65
r_angle_other_deg1.496
r_chiral_restr0.088
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms10088
Nucleic Acid Atoms
Solvent Atoms917
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing