7Z5S

Crystal Structure of botulinum neurotoxin A2 cell binding domain in complex with GD1a


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP289.150.2 M Lithium citrate tribasic tetrahydrate 20 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.6366.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.068α = 90
b = 105.068β = 90
c = 132.58γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2021-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
12.1105.071000.9911.127.383782
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)
12.12.141000.40.921.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5MOY2.1105.06883719416699.9810.190.18830.226446.052
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]
0.7470.747-1.493
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.864
r_dihedral_angle_other_3_deg16.632
r_dihedral_angle_3_deg15.987
r_dihedral_angle_4_deg15.785
r_lrange_it8.938
r_lrange_other8.927
r_dihedral_angle_1_deg7.908
r_scangle_it7.251
r_scangle_other7.25
r_mcangle_it5.564
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.864
r_dihedral_angle_other_3_deg16.632
r_dihedral_angle_3_deg15.987
r_dihedral_angle_4_deg15.785
r_lrange_it8.938
r_lrange_other8.927
r_dihedral_angle_1_deg7.908
r_scangle_it7.251
r_scangle_other7.25
r_mcangle_it5.564
r_mcangle_other5.564
r_scbond_it4.878
r_scbond_other4.877
r_mcbond_it3.905
r_mcbond_other3.897
r_angle_other_deg2.272
r_angle_refined_deg1.616
r_nbd_other0.316
r_symmetry_nbd_other0.217
r_nbd_refined0.196
r_nbtor_refined0.173
r_xyhbond_nbd_refined0.16
r_symmetry_xyhbond_nbd_other0.159
r_symmetry_xyhbond_nbd_refined0.146
r_symmetry_nbd_refined0.143
r_symmetry_nbtor_other0.077
r_chiral_restr0.071
r_bond_other_d0.034
r_bond_refined_d0.01
r_gen_planes_other0.01
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6733
Nucleic Acid Atoms
Solvent Atoms291
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing