7N7B

crystal structure of the N-formyltrasferase HCAN_0200 from Helicobacter canadensis on complex with folinic acid and dTDP-3-aminofucose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7N7A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529311-14% PEG-8000, 2% DMSO, 100 mM homopipes (pH 5). Crystals soaked in 26% PEG-8000, 600 mM NaCl, 5 mM folinic acis, 10 mM dTDP-Fuc3N, 100 mM MES (pH 6)
Crystal Properties
Matthews coefficientSolvent content
2.6854.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.264α = 90
b = 74.023β = 114.01
c = 82.996γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON II2019-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
125096.60.07413.55.645715
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1930.3342.83.5

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT7n7a229.6443385233096.590.19540.19240.2531RANDOM30.505
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.877
r_dihedral_angle_4_deg17.53
r_dihedral_angle_3_deg15.512
r_dihedral_angle_1_deg8.419
r_angle_refined_deg1.52
r_angle_other_deg1.268
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.877
r_dihedral_angle_4_deg17.53
r_dihedral_angle_3_deg15.512
r_dihedral_angle_1_deg8.419
r_angle_refined_deg1.52
r_angle_other_deg1.268
r_chiral_restr0.066
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4480
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing