8BJI

chimera of ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo fused to a proline-Rich-Domain (PRD) and profilin, bound to ADP-Mg-actin and a sulfate ion


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.529330% peg 4000, 0.2 M Lithium Sulfate (LiSO4), 0.1 M TrisHCl pH8.5
Crystal Properties
Matthews coefficientSolvent content
2.2545.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.974α = 90
b = 62.854β = 90.28
c = 93.588γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.979SOLEILPROXIMA 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
11.6461.8194.60.1238.578383726
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)
11.641.821.0941.6

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 REPLACEMENTTHROUGHOUT2PAV1.7525.0682105414185.40.17720.17530.2121RANDOM30.28
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]
0.09370.48110.171-0.2647
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion15.83
t_omega_torsion3.31
t_angle_deg0.92
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_torsion15.83
t_omega_torsion3.31
t_angle_deg0.92
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 Atoms6726
Nucleic Acid Atoms
Solvent Atoms944
Heterogen Atoms125

Software

Software
Software NamePurpose
BUSTERrefinement
AutoProcessdata processing
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing