X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NM7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15Morpheus I condition F3: 0.12 M monosaccharides [0.2 M D-glucose; 0.2 M D-mannose; 0.2 M D-galactose; 0.2 M L-fucose; 0.2 M D-xylose; 0.2 M N-acetyl-D-glucosamine] 0.1 M buffer System 1 [1.0 M imidazole; MES monohydrate (acid) pH 6.5], 30% v/v Precipitant Mix 3 [40% v/v glycerol; 20% w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
5.3276.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.928α = 90
b = 106.928β = 90
c = 369.259γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS EIGER X 16M2019-03-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.9537Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.9949.0499.90.5210.5350.1240.9746.618.526401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.993.1799.53.4033.5090.8410.55417.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5NM72.9949.041.9226300133399.910.23460.23260.272262.27
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d4.8405
f_angle_d0.5187
f_chiral_restr0.0362
f_plane_restr0.0036
f_bond_d0.0024
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3982
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms24

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing