X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6O18PDB entry 6O18

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298250 nL 20 mg/mL wild-type AlfC + 250 nL mother liquor (18% w/v PEG3350, 0.1 M Bis-Tris propane, pH 7, 20 mM sodium/potassium phosphate, 1% v/v glycerol), crystals appeared after five days, were harvested in mother liquor + 20% v/v glycerol + 10 mM alpha-L-fucose for ~1 minute, then flash-cooled
Crystal Properties
Matthews coefficientSolvent content
2.6152.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.983α = 90
b = 138.236β = 90
c = 264.44γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2017-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033202APS23-ID-B

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
12.629.8499.70.0560.0630.0280.99813.44.850905
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)
12.62.681001.2921.4370.6190.4845.1

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 REPLACEMENTTHROUGHOUTPDB entry 6O182.629.8448372248699.450.20870.20780.2262RANDOM101.99
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]
-0.85-1.922.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_dihedral_angle_3_deg17.214
r_dihedral_angle_4_deg10.419
r_dihedral_angle_1_deg6.594
r_angle_refined_deg1.269
r_angle_other_deg1.262
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_dihedral_angle_3_deg17.214
r_dihedral_angle_4_deg10.419
r_dihedral_angle_1_deg6.594
r_angle_refined_deg1.269
r_angle_other_deg1.262
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10198
Nucleic Acid Atoms
Solvent Atoms13
Heterogen Atoms44

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction