8WEX

Crystal structure of N-acetyl sugar amidotransferase from Legionella pneumophila


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelRoseTTAFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION28720% (w/v) PEG 3350, 0.2 M ammonium acetate
Crystal Properties
Matthews coefficientSolvent content
2.3647.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.722α = 90
b = 74.722β = 90
c = 319.678γ = 120
Symmetry
Space GroupP 32 1 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97914SSRFBL17U

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
12.3345.671000.99819.817.244179
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)
12.332.390.602

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 REPLACEMENTTHROUGHOUT2.332041846214199.510.209860.20790.24687RANDOM51.194
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]
0.170.080.17-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_4_deg19.173
r_dihedral_angle_3_deg17.37
r_long_range_B_refined8.177
r_long_range_B_other8.167
r_dihedral_angle_1_deg6.477
r_scangle_other5.979
r_mcangle_it5.329
r_mcangle_other5.329
r_scbond_it3.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.114
r_dihedral_angle_4_deg19.173
r_dihedral_angle_3_deg17.37
r_long_range_B_refined8.177
r_long_range_B_other8.167
r_dihedral_angle_1_deg6.477
r_scangle_other5.979
r_mcangle_it5.329
r_mcangle_other5.329
r_scbond_it3.783
r_scbond_other3.783
r_mcbond_it3.577
r_mcbond_other3.577
r_angle_other_deg2.273
r_angle_refined_deg1.234
r_chiral_restr0.064
r_bond_other_d0.035
r_gen_planes_other0.008
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms6236
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
autoPXdata reduction
pointlessdata scaling
MR-Rosettaphasing