8QFT | pdb_00008qft

X-ray structure of non-toxic non-hemagglutinin (NTNH) protein from botulinum neurotoxin serotype X


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BYP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529415 mg/ml NTNH/X in 20 mM MES pH 5.5, 150 mM NaCl, 0.5 mM TCEP mixed in 2:1 volume ratio with 90 mM MES/imidazole pH 6.5, 9% (w/v) PEG 4,000, 18% (v/v) glycerol, and 3% (w/v) dextran sulfate sodium salt
Crystal Properties
Matthews coefficientSolvent content
4.472.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.106α = 90
b = 174.106β = 90
c = 138.023γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2019-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
13.387.051000.2020.2080.0470.999719.336727
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)
13.33.451002.7722.8590.6990.92416.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3.373.7436531193999.5260.2790.27630.290.33260.34220.051
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]
9.3014.6519.301-30.173
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_other37.622
r_lrange_it37.621
r_mcangle_it26.686
r_mcangle_other26.684
r_scangle_it26.536
r_scangle_other26.535
r_mcbond_it17.506
r_mcbond_other17.506
r_scbond_it16.783
r_scbond_other16.782
RMS Deviations
KeyRefinement Restraint Deviation
r_lrange_other37.622
r_lrange_it37.621
r_mcangle_it26.686
r_mcangle_other26.684
r_scangle_it26.536
r_scangle_other26.535
r_mcbond_it17.506
r_mcbond_other17.506
r_scbond_it16.783
r_scbond_other16.782
r_dihedral_angle_6_deg14.168
r_dihedral_angle_3_deg14.157
r_dihedral_angle_1_deg6.167
r_dihedral_angle_2_deg3.892
r_angle_refined_deg1.044
r_angle_other_deg0.616
r_nbd_other0.283
r_symmetry_nbd_refined0.266
r_symmetry_nbd_other0.23
r_symmetry_xyhbond_nbd_refined0.223
r_nbd_refined0.196
r_xyhbond_nbd_refined0.191
r_nbtor_refined0.186
r_symmetry_xyhbond_nbd_other0.09
r_symmetry_nbtor_other0.08
r_chiral_restr0.049
r_gen_planes_other0.005
r_bond_refined_d0.004
r_gen_planes_refined0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9710
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing