8BR1

ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to Latrunculin-B-ATP-Mg-actin, and 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE and 2 Mg ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PAV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529326 % peg 3350, 26 % Glycerol, 30 mM LiSO4, 0.1M TrisHCl pH8.5, 3 % Dioxane,
Crystal Properties
Matthews coefficientSolvent content
2.5852.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.116α = 90
b = 132.443β = 110.57
c = 96.396γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.9786SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.04447.7684.30.16214.132.78649554.49
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.0442.2128.53.852

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 REPLACEMENTTHROUGHOUT2PAV2.04447.7686494430276.70.19160.190.2221RANDOM61.71
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]
1.4461-0.4354-0.1995-1.2466
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17
t_omega_torsion3.1
t_angle_deg0.93
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion17
t_omega_torsion3.1
t_angle_deg0.93
t_bond_d0.008
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11956
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms200

Software

Software
Software NamePurpose
BUSTERrefinement
AutoProcessdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing