5LQ7

Salmonella effector SpvD - G161 variant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5277100 mM Tris, 200 mM NaCl, 22 % PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.0740.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44α = 90
b = 51.97β = 107.7
c = 47.22γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.651.9799.40.10410.45.926737
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)
11.61.6999.20.5791.96

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 REPLACEMENTTHROUGHOUT5LQ61.644.9825387133399.230.16490.163190.1973RANDOM20.415
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]
0.21-0.73-0.240.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.51
r_dihedral_angle_3_deg13.563
r_dihedral_angle_4_deg9.048
r_long_range_B_refined7.76
r_long_range_B_other7.758
r_scangle_other6.2
r_dihedral_angle_1_deg5.835
r_scbond_it4.026
r_scbond_other4.021
r_mcangle_it3.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.51
r_dihedral_angle_3_deg13.563
r_dihedral_angle_4_deg9.048
r_long_range_B_refined7.76
r_long_range_B_other7.758
r_scangle_other6.2
r_dihedral_angle_1_deg5.835
r_scbond_it4.026
r_scbond_other4.021
r_mcangle_it3.256
r_mcangle_other3.255
r_mcbond_it2.225
r_mcbond_other2.224
r_angle_refined_deg1.41
r_angle_other_deg0.987
r_chiral_restr0.104
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.006
r_gen_planes_other0.002
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 Atoms1664
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing