4DTF

Structure of a VgrG Vibrio cholerae toxin ACD domain in complex with AMP-PNP and Mg++


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DTD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.3293mixing 300 nL of protein at 13mg/mL with 100 nL of 2.4 M AmSO4, 0.1 M Bi-Tris pH 6,3., temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.6165.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.39α = 90
b = 128.39β = 90
c = 76.58γ = 90
Symmetry
Space GroupP 43 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMIRRORS2012-01-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEOTHER

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
12.12501000.06826.115.63696328.97
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)
12.122.1796.40.484.314

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DTD2.1245.393681336813128499.80.1780.1770.199RANDOM30.67
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]
-2.7756-2.77565.5512
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.19
t_omega_torsion3.27
t_angle_deg1.06
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion19.19
t_omega_torsion3.27
t_angle_deg1.06
t_bond_d0.009
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
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 Atoms2757
Nucleic Acid Atoms
Solvent Atoms504
Heterogen Atoms59

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling